Puzzle Link is a game where blocks of matching color have to be dissolved. New blocks constantly scroll into the screen from the top. The game is over when the first blocks reach the bottom of the screen. You can dissolve blocks by shooting at them. The shots form a line where they impact. If that line connects otherwise unconnected blocks of the same color they will dissolve.

There are three different modes: In "Normal" you have to link two special blocks that appear after some time. If you manage to finish the level within the time limit you will unlock one of 50 collectible cards. In "Clear Mode" you have to clear a given constellation of blocks. "Battle Mode" is a two player link-cable mode.