The invention relates to a satellite-borne computer autonomously computer switching system based on an FPGA, which monitors the working state of the current working computer by adopting a hardware watch dog, a dog biting counting module and a continuous dog biting identification module; when dog biting for one time is monitored, the current working computer is reset; when the second-time dog biting is monitored continuously in a certain time period t, the current working computer is switched into a standby engine; when the time interval of two-time dog biting is more than t, only the current working computer is reset and the computer switching is not implemented; the system also monitors the accumulated faults of the current working computer by adopting a dog biting accumulating counting module; and when the accumulated fault times are more than the set value N, the computer switching is implemented. The system can effectively monitor the faults of the satellite-borne computer, and effectively reduce the time for the computer switching on the basis of eliminating faults.