As you progress through the story, there are a few castles and areas which become blocked off to the player after finishing the questlines associated with them. However, there is a simple-to-perform glitch that allows the player to access these areas again. While on horseback, the player must back their horse as far as possible into the gate of a blocked building and fire a bomb arrow at the ground in front of them, this will cause the player to fly back and clip through the gate with ease.

As of August 2020, an interesting glitch could happen after performing a certain killing blow. Sometimes after defeating an enemy there is a chance that they will start crawling around until the player finishes them off. After performing a beheading kill on your foe, a technique meant to be a killing blow, there is a glitch that can happen which causes them to still crawl around on the ground as if they were defeated in a normal fashion. It is currently unclear if this glitch has been patched out since.

Located behind the Speak No Evil monkey statue on the island of Saruiwa, the player can find a painting of a hand with an image of a Pagoda in the palm. This is a reference to a symbol/graffiti of a hand that's found in Infamous: Second Son as well as the cover of that game's collector's edition.

On the southwestern island of Saruiwa of Iki Island, if the player follows a certain path up on the way to the monkey shrine, they can find a small painting on a rock wall of a two-headed bird in the shape of a star. This is a reference to the graphic on the back of Delsin Rowes jacket and the symbol for the Karma system used in InFAMOUS Second Son.

Located near the See No Evil monkey statue on the island of Saruiwa, a wall painting can be found depicting a man with a two pronged sword and lightning powers. This is a reference to Cole MacGrath, the protagonist of the first two games in the InFAMOUS series.

On Iki Island underneath the Shrine of Shadow, a small cave can be found containing some supplies and a canvas painting on a table. This painting depicts 3 animals: a hippo, a raccoon or tanuki, and a turtle. This is a reference to Murray, Sly and Bentley from the Sly Cooper series.

On Iki Island, if you follow the Eastern stream of Kitsune Pond, you will come across a small climbable waterfall with a secret entrance behind it. Once squeezed through, the player will find the "Demonic Archer's Mask" and art on the wall to the left depicting Sly, Murray, and Bentley from the Sly Cooper series in a traditional Japanese art style.

A sword kit named "The Stonecutter" can be obtained at the Zasho River Pillar of Honor. Its description reads: "Humble, but more powerful than a prince". The sword name and description are possibly a reference to a story by the same name contained in Andrew Langs' The Crimson Fairy Book. In the story, a humble stonecutter wishes to be turned into many things that hold power by a mountain spirit, the first of which being a prince. In the end, he wishes to be changed back to his original form realizing that he is satisfied living as a humble stonecutter.

After the game's release, Nate Fox (game director) and Jason Connell (creative director) were appointed as permanent ambassadors of tourism for Tsushima Island in Nagasaki, Japan by the Mayor of Tsushima, Hiroki Hitakatsu.

In September of 2020, a typhoon toppled a torii gate at the Shinto Shrine of Watatsumi on the island of Tsushima. A few months later in November of 2020, a priest from the shrine, Yuichi Hirayama, created a fundraising campaign page to help rebuild said torii gate. Fans of Ghost of Tsushima flooded the campaign page and smashed the goal amount of ¥ 5 million Yen (about $48,000 USD) eventually hitting over 20 million Yen by the end of December 2020. After the reconstruction finished, the shrine became a popular tourist destination until March 23, 2025, when the shrine's management announced a ban on domestic and international tourists. They would only allow parishioners and worshippers to visit from that point on due to an undisclosed incident the day prior, as well as recurring instances of vandalism and verbal abuse against staff by Korean tourists.

In response to Ghost of Tsushima's popularity, Nagasaki Prefecture of which the island of Tsushima is governed under, created a website to help encourage tourism to the island. It explores historical sites that show up in the game, local foods, and activities to partake in on the island that also involve locations depicted in the game.

A sword kit named, "Ōmukade's Revenge", can be obtained by completing the mythic tale "The Spirit of Yarikawa's Vengeance". The design on the sword wrap depicts a coiling giant centipede. This is possibly a reference to the Japanese folktale of Tawara Tōda Monogatari in which a giant centipede (mukade or Ōmukade in Japanese) yokai terrorizes a kingdom.

The Kidafure Battleground located at the center of Iki Island contains a few overgrown buildings. These are based on a few of the replica buildings placed around the Harunotsuji Archeological Museum located in the real Iki Island in Japan.

Located in the Southwest region of Iki Island is a rocky island called "Saruiwa", which translates to "monkey rock", the word 'saru' meaning monkey and the word 'iwa' meaning rock. It is named as such because the rock formation resembles a monkey. This island is also named after and based on the Saruiwa rock formation found on the real Iki Island in Japan, though it should be noted that the in-game location and real-life location do not match up geographically.

In an interview with Nate Fox, Ghost of Tsushima's creative director, he said that:

"The game was definitely scripted to provide more storms as you do things which are extremely Ghost driven".

This is referring to the change in weather that can happen throughout the game, becoming more stormy and violent as Jin uses more "dishonorable" Ghost techniques over his traditional Samurai techniques. This adds to the theme of Jin losing his way as a samurai to protect his homeland of Tsushima.

Located atop the Omi Monastery temple in the Toyotama region you can find a piece of vanity Gear called the "Band of the Second Son". The design is reminiscent of the beanie worn by Delsin Rowe, the protagonist of another Sucker Punch production, Infamous: Second Son.

In the Iki Island expansion, there is a special Horizon Forbidden West-themed armor set that can be obtained at the Forbidden Shrine. At the shrine, there is a scroll containing a poem hinting at how to do so. Spoiler:The player must equip Tadayori's armor and activate focus hearing to reveal 3 targets along the shrines statue: one above it's head, another on its hand, and the last on the head of a demon that the statue is standing on. Once completed, the corruption wrapped around the statue falls away and the player receives said armor

The corruption wrapped around the statue is a reference to all the corruption tainting the land and machines in Horizon Zero Dawn and Horizon Forbidden West.

In the Iki Island expansion, there is a special Bloodborne-themed armor set that can be obtained at the Blood-Stained Shrine. At the shrine, there is a scroll containing a poem hinting at how to do so. Spoiler:The player must take damage in front of the shrine before equipping the Kensei armor and healing themselves, this will unlock the Yharnem armor.

At the base of the shrine there is also a painting of a giant red circle with black birds flying in front of it. This is a reference to the giant blood moon featured throughout Bloodborne.

In the Iki Island expansion, there is a special Shadow of the Colossus-themed armor set that can be obtained at the Shrine in Shadow. At the shrine, there is a scroll containing a poem hinting at how to do so. Spoiler:The player must equip the Ghost armor and thrown down a smoke bomb in front of the shrine to obtain this armor set.

The shrine is also adorned with a glowing symbol and some fur patches, two characteristics that are seen on every colossi throughout the referenced game, Shadow of the Colossus.

In the Iki Island expansion, there is a special God of War-themed armor set that can be obtained at the Shrine of Ash. At the shrine, there is a scroll containing a poem hinting at how to do so. Spoiler:The player must equip the Sakai Clan armor and perform the action for unsheathing their sword in front of the shrine to obtain it.

There is also an ash tree with a golden hand print planted near the shrine, a direct reference to the intro for God of War.

Laying along the base of the statue are piles of chains, these are a reference to the chains that hang from the hilts of one of Kratos signature weapons, The Blades of Chaos.