Pikmin 3 expands on the gameplay of the previous Pikmin titles, in which the player directs a horde of up to 100 plant-like creatures called Pikmin. The Pikmin can be directed to accomplish various tasks, such as building bridges, destroying barriers, and defeating enemies. The Pikmin themselves come in various types that signify their special abilities or immunities to hazards. While Red, Yellow, and Blue Pikmin return from previous Pikmin games, Pikmin 3 introduces at least two new Pikmin types, Rock Pikmin, which are used to smash through tougher barriers, and the other is a pink, flying pikmin that is currently unnamed and is spotted in the start screen animation of the developer demo.  When questioned about the presence or absence of the Purple and White Pikmin types featured in the second game, Miyamoto stated that "They're in there somewhere, just hidden...".

The player controls four different leaders of the Pikmin at once, compared to its predecessor Pikmin 2 in which two leaders were present. Captain Olimar, the protagonist of previous Pikmin titles, is not playable for currently unknown reasons. Pikmin 3 offers two control schemes: the Wii U GamePad or the Wii Remote with the Nunchuk accessory. In both cases the Wii U GamePad gives the player an overhead map of the game environment, visible on its touch screen.