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Aiming at the problems of low accuracy and long detection time caused by noise in the current spacecraft communication signal equipment fault detection system, a fault detection system of spacecraft communication signal equipment based on CPCI bus is designed. The CPCI fault simulation module uses RS232 serial line to control the injector, uses the fault injector to execute fault injection into CPCI bus, receives control system parameters and instructions, uses clock distribution chip to transmit clock signal, detects board module through CPCI, realizes interface control with FPGA, and completes system hardware structure design. By using the interdependence between tasks, the mutual detection between tasks is realized. Through the terminal network workstation, the relevant information of multi-channel communication network is regularly sent, and the defect free detection results are returned. The secondary correlation algorithm is used to extract the detailed information of multi-channel communication fault signal, accurately estimate the communication signal delay, eliminate the communication fault caused by multi-channel network noise, and complete the system software department sub design. The experimental results show that the system designed in this paper has high detection accuracy and can effectively shorten the detection time of communication equipment fault signal.