Atomix takes place on a playfield consisting of a number of walls, with the atoms scattered throughout.
The player is tasked with assembling a molecule from the atoms. The atoms must be arranged to exactly match the molecule displayed on the left side of the screen.
The player can choose an atom and move it in any of the four cardinal directions. A moved atom keeps sliding in one direction until it hits a wall or another atom.
Solving the puzzles requires strategic planning in moving the atoms, and on later levels with little free space, even finding room for the completed molecule can be a problem. Once the molecule is assembled, the player is given a score; the faster the puzzle was completed, the higher the score.

Each puzzle must be completed within a time limit. A portion of the player's score can be spent to restart a failed puzzle. The entire game consists of 30 puzzles of increasing difficulty.
In addition, after every five puzzles, there is a bonus level where the player must move laboratory flasks filled with various amounts of liquid to arrange them from empty to full.