Spider-Man 3 Puzzle is a match-three puzzle game based on the 2007 film featuring the comic hero. As in other match-three games, the player is presented with a grid of tiles (here called tokens) that can be removed by making matches of three or more tiles of the same colour. What makes this variant of the concept different is that the objective isn't just to remove the tokens but to move Spider-Man across the grid to a special destination. Each level has a path that Spider-Man follows. The path is hidden and is only revealed by swapping and removing tokens that are over the path. Spider-Man moves automatically when the path is revealed. Each level is time-based and Spider-Man has to reach his destination before the timer runs out.

The game features some special power-up tokens that will help the player. For example, there are the scramble tokens that shuffle all tokens on the grid, the spider-sense tokens that reveal the path temporarily, and the rage tokens that can be used to plough through tokens blocking the path. Spider-Man will be chased by black goo on some levels and has to finish the levels before being caught.