The following differences and new features are included in Ocarina of Time 3D.
- The Master Quest is included, but it's only unlocked after you finish the original version.
- The bow, boomerang, and slingshot can be aimed by moving the 3DS around, using the gyroscopic technology of the 3DS. There is also the option to aim it in the classic way with the D-pad like in the original.
- There is a Sheikah Stone near Link's house in Kokiri Forest, and another in the Temple of Time. You can crawl into these to see Sheikah Stone Visions, which are short video sequences that provide hints if you're stuck.
- There is a Boss Challenge mode that you unlock after finishing the first temple after you get the Master Sword. This mode allows the player to fight an individual boss or all of the bosses in order, at any time.
- The Stone of Agony is now the Shard of Agony, which plays a tone when secrets are nearby, since the 3DS doesn't include a rumble feature.
- The touch screen can be used to change Link's equipment.
- The graphics have been improved, with better textures, more polygons, and more natural movement by the game's characters.