The invention provides a substation computer monitoring system and method. The system comprises a monitoring and control device, a man-machine interface configuration module, an automatic IED (Intelligent Electronic Device) model configuration module, an automatic version matching module, a protocol converter, an adaptive communication module of the protocol converter, and a background monitoring subsystem, wherein the monitoring and control device, the man-machine interface configuration module, the automatic IED model configuration module, the automatic version matching module, the protocol converter and the adaptive communication module of the protocol converter are connected with the background monitoring subsystem respectively. The system has the benefits that the substation configuration information can be set by a user according to the specific demand, and a corresponding background monitoring subsystem interface can be quickly displayed; IED performance description files and mapping files can be quickly generated according to different configurations, so that the manual workload is greatly reduced, the error probability is reduced, and the labor cost is reduced; existent hardware problems can be detected in advance and corresponding strategies can be found; the matching situation of the software versions of the background monitoring subsystem and the monitoring and control device can be mastered in time.