The invention provides a self-diagnosis method and system for internal functions of an FPGA (Field Programmable Gate Array). The method comprises the steps of adding a CRC (Cyclic Redundancy Check) sum to input messages of the FPGA, performing CRC on output messages of the FPGA, counting the number of CRC error messages in the output messages of the FPGA, judging whether the FPGA is continuously abnormal or not through a leaky bucket algorithm according to the number of CRC error messages, and sending out an alarm signal when the FPGA is continuously abnormal. Whether the FPGA is continuously abnormal or not is judged by adopting the CRC and the leaky bucket algorithm in the whole process, and an alarm signal is sent out when the FPGA is continuously abnormal, so that self-diagnosis of the internal functions of the FPGA is realized, and the reliability of the FPGA is effectively improved.