This paper focuses on spaceborne information processing and control system based on microsystem technology that used to reach the goals of miniaturization, high reliability, high performance and efficient thermal management of space equipment. Firstly, the architecture of data processing and control system based on the new spaceborne devices are introduced. Then, the 3D micro-nano integration technology, which is based on wafer level processing, chip stacking, micro bump preparation and micro assembly, is used to reduce the size of the core hardware of the system to 20% of the original size, thus greatly reducing the volume, size and weight. In this paper, high thermal conductivity packaging materials are used to reach the goals of efficient thermal management of spaceborne electronic system. A new general solution for the design and implementation of spaceborne information processing and control microsystem is proposed. The advantages of this solution in miniaturization, high reliability, high performance and efficient thermal management are verified by hardware in the loop Demo system.