Mario vs. Donkey Kong: Mini-Land Mayhem! is a platform game with a 2D level design. Similar to the old Lemmings games, the puzzle-based gameplay in Mini-Land Mayhem is built upon that of the 2 earlier Mario vs. Donkey Kong titles, where players do not control Mario, but instead are tasked with guiding wind-up miniatures to level exits, in this case mechanical Mini-Mario toys. The game requires players to "build and rebuild levels on the fly," to allow the small miniature Marios to get from point A to point B. As the mini-Marios cannot be directly controlled, the player instead uses a stylus to manipulate their movements. Each level has one to three minis that must be moved, and it is necessary to rescue all the minis to clear a level, and each exit closes several seconds after a mini enters. If a mini falls onto spikes, traps, pitfalls, run into enemies, falls from a height of ten blocks or more, or the timer runs out, the player gets a game over and can either restart or exit the level. Once a single mini has reached the door, a timer comes on, and everyone else must be through the door within about six seconds, otherwise, the door will lock up, leaving out any other mini toys behind and it's Game Over. Unlike Minis March Again! and previous installments of the series, it is not possible to stop the miniatures or change their direction once they are activated.
There are eight themed "worlds" in the theme park, with eight levels each leading to boss battles. A zoomed-out map view on the upper screen helps players navigate worlds. Each world has a different type of object to interact with. The first world involves building walls and floors, using red girders to serve as bridges, walls, and ramps. Later players gain access to magnets, conveyor belts, and springs, as well as other building blocks for directing the robot army such as trampolines and repositioned platforms. Each world requires the player to use that world's specific tool to defeat Donkey Kong in the boss battle. For example, in one level, platforms can be built so the Mini-Marios can get to Donkey Kong to electrocute him or drop bombs on him. There is a time limit of 300 seconds and the player has six mini Marios to start with, just like the previous game. To clear the fight, the Mini-Marios need to hit Donkey Kong with three different objects or stepping on three switches (six times in the final battle). If the player loses all their Mini Marios or runs out of time, the player receives a Game Over. If the player loses to Donkey Kong by losing all six Mini Marios, the circle shows Donkey Kong as he beats his chest and Pauline calls for Mario, while the "GAME OVER!" text appears on the bottom of the screen, and any Mini Marios that attacked Donkey Kong will freeze. If the player loses the battle by getting a time-up, the same thing happens, except the "TIME'S UP!" text appears on the bottom screen, but Donkey Kong will say his voice earlier, and Pauline calls for Mario afterwards. There are also items like hammers, which can hit Circus Kong and other gorilla robots out of the way.
There are multiple solutions to many of the levels, although there are rewards for creating the optimum route. There are over 200 levels, and players are awarded trophies and medals for speed runs and gathering collectibles. Overall, you can collect coins, M-tokens, and Mario Cards. There are also unlockable mini-games. In the plus mode, the levels are slightly harder, as the minis must be brought in the right order as shown at the beginning of the level. If a mini goes in the door in the wrong order, an X is displayed on the mini toy that went in the player's own exit order, resulting in a Game Over.