Multi-motor synchronous control has always been one of the key technologies in the field of motion control. It is widely applied in automatic control of printing, paper making and filament winding. In this paper, an embedded multi-motor synchronous motion controller based on DSP and FPGA with pulse sequence is designed. The overall architecture and design ideas of controller is proposed, and some key technologies, which include motion pulse generator, pulse compensation planning and pulse output modulation, have been solved. Meanwhile, through experiments it shows that the designed controller can achieve high synchronization accuracy in high-speed conditions.