A debugging method for a computer system is disclosed, which includes defining a debug reference data area in a storage device for a BIOS and a control device, periodically transmitting a reply request including an identification information to the BIOS, transmitting reply information corresponding to the identification information according to the reply request, checking the reply information and storing an execution log data into the debug reference data area when the identification information does not conform to the original identification information, determining whether the computer system is in normal operation, and performing a debugging process according to the execution log data when the computer system is in abnormal operation.