The invention discloses an intelligent substation process layer physical link fault positioning system. The system comprises a fault positioning host, a network monitoring management data cloud, a process layer switch and an intelligent electronic device. The fault positioning host is used for generating an actual process layer network communication physical link topological graph, comparing a preset process layer network communication physical link topological graph with an actual process layer network communication physical link topological graph to realize fault positioning, and monitoringnetwork flow abnormity and network storm link faults; the network monitoring management data cloud is used for receiving network monitoring data and fault positioning data of the fault host and forming a fault analysis report; the mapping relation of the process layer network communication physical link is vividly displayed in a graphic mode, and real-time monitoring and fault positioning of the process layer network are achieved through comparison of the preset process layer network communication physical link and the actual process layer network communication physical link.