Anti-UAV system is of vital importance in countering air threat. Due to its special needs, the controller is required to possess the ability of processing complex data in high speed with high real-time and reliability at the meantime. According to the existing requirements, we developed a DSP + STM 32 dual core controller which have real-time control system for tasking schedule and ensuring the optimal real-time. This controller met the expected requirements by our experiments. The real-time control system helps to improve the reliability and real-time performance, and provides a broad idea for the similar design in the field of anti-UAV controller.