Caverns of Mars is a vertically scrolling shoot 'em up similar in concept and visual style to the 1981 arcade game Scramble. Christensen changed the orientation of the caverns from Scramble, having the player fly down into them as opposed to sideways through them. For technical reasons, vertical scrolling is somewhat easier than horizontal to implement on the Atari platform. Unlike Scramble, the targets generally did not move relative to the map.

Using a joystick, the player controls a ship descending into the tunnels of Mars, firing at targets along the way. The player's spacecraft features two cannons, positioned on either side of the craft, firing downwards. The player needs to avoid hitting the cavern walls, while shooting targets of opportunity along the way. Fuel tanks can be shot to add 5 points of fuel, and the craft is destroyed if it runs out.

There are several different sections of the map, with easier skill levels removing the more difficult sections from the areas through which the player has to fly. The easiest skill level has only three sections, the hardest has six. On any skill level the last section of the map is a reactor, which the player lands on and thereby sets to explode. The player then has to reverse course and fly up and out of the caverns to escape before the reactor explodes.