Super Mario 3D Land is a platform game that has been described by game designer Shigeru Miyamoto as a "3D Mario that plays as a 2D Mario game".[7] As such, Super Mario 3D Land combines the elements of traditional side-scrolling video game titles, such as linear-based levels, with those of the modern open world titles, such as moving Mario in three dimensions and performing a variety of actions.[7] Similar to the older side-scrolling Mario games, the health system revolves around Mario shrinking upon taking damage from enemies or hazards, there is a dedicated "Dash" button as opposed to using analog input to determine travel speed, and damage as "Small Mario" results in losing a life. Mario has also learned two new moves: a barrel roll and a roll jump, the former of which can be used to break blocks in a similar manner to jumping at blocks from below or ground pounding, and the latter allowing Mario to cover much horizontal ground in one jump. Super Mario 3D Land utilizes a similar level objective to the aforementioned side-scrolling games, in which the point of each level is to reach and grab the "Goal Pole" at the end of the level, within the time limit.[7][8]

The game offers a number of traditional Mario items, such as the Super Mushroom, Fire Flower and Starman, along with new power-ups that bestow special suits onto Mario and grant him new abilities.[9] Returning from Super Mario Bros. 3 is the Super Leaf power-up, which gives Mario the Tanooki suit, allowing him to float in the air and attack with his tail, with a later variant also allowing him to transform into a statue upon performing a ground pound.[10] The player is able to reserve an extra power-up, which can be retrieved by tapping the item visible on the touchscreen.

Other items include the Boomerang Flower, which allows Mario to throw boomerangs that can collect out-of-reach items and attack enemies; the Propeller Box, which allows Mario to reach high places; and the rare Prize Box, which gives Mario extra Coins while walking around in it.[9][11] The Invincibility Leaf, which appears after the player dies five times in a level, gives Mario invincibility and Tanooki Suit abilities; while the P-Wing, which appears after the player dies ten times in a level, sends the player right to the end of the level, near the Goal Pole. (The invincibility leaf and the P-wing are only available in regular worlds) [12] Each course contains three hidden Star Medals that are required to unlock certain levels.[13] The map screen also contains Toad Houses where players can visit Toad and receive additional items, and Mystery Boxes where more Star Medals can be earned. After clearing the game once, a set of "Special" levels are unlocked, some of which contain additional challenges, such as a 30-second time limit.[14] Clearing the S1 castle unlocks Luigi as a playable character, who has slightly different handling to Mario.[10]

Super Mario 3D Land utilizes the Nintendo 3DS's autostereoscopic technology, allowing players to perceive depth when viewing the game screen. While the game is designed to not require the 3D effect, some obstacles or points of interest are deliberately more noticeable or easier when the 3D is switched on.[7] Super Mario 3D Land also utilizes optional use of the 3DS gyroscope, which can be used to control cannons and binoculars.[7] The game also features StreetPass functionality, allowing players to exchange Mystery Boxes containing bonus items.[12] StreetPass also gives players another Toad house so they can get items.[12]