Abstract: As the “main switch” of the forth phase of China’s lunar exploration projects, Queqiao-2 relay satellite not only needs to support relay communication for Chang’E-6 and Chang’E-7 mission, but also needs to support Change’s-8 in the future and take over from Chang’E-4 mission. At the same time, the relay satellite itself carries multiple scientific payloads such as the Earth Moon VLBI experimental system to support scientific research and experiments in the Earth Moon space. A high-performance, highly integrated, and highly reliable integrated comprehensive data processor is proposed and implemented for the Queqiao-2 relay communication system to meet the multi task requirements of deep space exploration tasks, and to address the challenges it faces in complex space environments such as resource constraints, high reliability, and long lifespan. On the basis of Chang’e-4 relay satellite, a comprehensive functional upgrade has been carried out, with more technical status, stronger functions, and more complex interfaces. A deep space exploration system with over 8 Gb/s storage, calculation, and control integration has been implemented and verified in orbit, and software in orbit reconfiguration is supported. The ground return capability covers 1-500 Mb/s for the first time, effectively supporting the smooth execution of the Chang’E-6 human’s first lunar far side sampling and return mission. The design method can provide reference for data processing and transmission design of subsequent deep space exploration missions.