Super Zaxxon is similar to the original Zaxxon, running on identical hardware and having almost identical gameplay. Like its predecessor the game uses isometric projection, where the player can not only control the ship's left and right movements, but also adjust its height. Primarily Super Zaxxon offers slightly faster gameplay, a different set of graphics, different stage layouts and a few more enemies (including the "Mine Layer" in level 2, and indestructible turrets in level 1). The game is otherwise structured very similarly and has similar goals, but is considered to be the harder game of the two.

In the original Zaxxon, the player is confronted at the end by a large walking machine (called Zaxxon). In Super Zaxxon, it is three robot dragons, with Zaxxon not appearing in the game at all. There are also no space battles in Super Zaxxon, with all action taking place on an asteroid base.