Abstract: The active beam scanning system for heavy ion therapy has some advantages in some respects. In order to achieve spot scanning using pencil beam for heavy ion therapy, the control system needs to control scanning magnet. The therapy plan generates dose data and tumor area therapy data, and transmits them to the dose controller and spot scanning controller. At the same time, the accelerator control system transmits synchronous timing event data to the spot scanning controller, then the spot scanning controller waits for synchronous trigger from the synchronous timing system. When the dose controller sends trigger plus to the spot scanning controller, the spot scanning controller needs to change spot based on the tumor area therapy data, and curves it by interpolation algorithm. The dose controller counts dose pluses from the front-end electronics of the gas ionization chamber. When therapy dose is over, the dose controller sends a plus to control the Faraday cup to block heavy ion beam to realize safe therapy by spot scanning. Experiments show that with the current running power supply, magnet devices, and beam quality, the spot scanning control system can control pencil beam scanning spot by spot between 2 mm.