High-precise and multi-axes motion control system is required in the application of semiconductor equipment and high-performance industrial equipment. To achieve the tight performance requirements, this paper presents the control system architecture, communication, and timing management solution. We use multiple cores DSP and FPGA as the main control chips, use SRIO @5Gbps *4 as the DSP and FPGA communication protocol, and use Aurora 8B/10B @5Gpbs as the inter-board communication protocol. This architecture with its high sampling rate and low latency can improve the motion control performance and raise the system sampling bandwidth. Analysis and test results of system communication and timing management are included to demonstrate the efficacy of the proposed scheme.