Taking advantage of the robustness of genetic algorithm and the advantage of FPGA in parallel computing, we developed the cavity failure compensation program based on the Injector II’s Cryogenic Module IV (CM4) of China Accelerator Driven Sub-critical System (C-ADS). The beam dynamics software TRACEWIN was used to verify the results got by the FPGA program, and the FPGA program was packed as an IP core to be used in a more general form in the embedded Linux system. In addition, considering the requirements of independence and low latency for the future superconducting cavity failure compensation system, Linux system and EPICS components are compiled for the MicroBlaze soft core processor, and the communication function of the superconducting cavity failure compensation system was verified in the built simulating communication environment.