A computer peripheral connecting interface system configuration debugging method and system is proposed, which is designed for use in conjunction with a computer platform that is equipped with a particular type of peripheral connecting interface, such as a PCI (Peripheral Component Interconnect) interface, for automatically finding errors in the PCI system configurations of a group of peripheral devices connected to the PCI peripheral connecting interface, and if errors are found, capable of automatically generating an electronic error report. This fully-automatic debugging capability can help software engineers to more conveniently and efficiently correct the errors in the PCI system configurations on a computer platform.