In order to solve the problem that the spacecraft control system is difficult to diagnose and locate fault quickly and accurately, a fault diagnosis method based on 3D correlation matrix is proposed. According to the functional principle of complex system, the optimal directed graph model of fault propagation of different states is established. According to the mapping relationship of the 3D correlation matrix and fast mapping of detection results to fault modes, it realizes the rapid diagnosis and location of system faults and the optimal design of test points. The results show that this method can minimize the number of test points, reduces the complexity of fault diagnosis system and improves the rapidity of diagnosis.