Mega Tower Assault is a tower defence game similar to Desktop Tower Defense or Fieldrunners. As with other games of its kind, the idea is to prevent wave after wave of enemy troops to get to the player's command center. This is done by building stationary turrets that automatically shoot at the enemies that come within their range. At the start of the game the player has a small sum of cash that can be spent on different turrets such as chain guns, missiles and flame throwers. By destroying enemy troops and surviving waves the player gets more money that can be used for building new turrets or upgrade old turrets.

The game consists of four different scenarios (beach, snow, platform and lava) each with three levels. A level consists of 20 or more enemy waves and once completed the next is unlocked. While the first scenario (beach) is straightforward tower defending the later scenarios adds additional level features that lead to further tactical considerations for the player. In the snow scenario enemy soldiers can travel safely underground while the platform levels feature conveyor belts that increase the speed of the troops. The lava levels feature platforms that can be moved around by the player. Some levels have neutral buildings that can taken over by engineers. The player then receivers a special function that can be used at any time, for example a rocket attack that destroys all enemy troops.