The invention discloses an intelligent substation process layer virtual connection fault positioning system, which comprises a virtual connection fault positioning system, a network monitoring management data cloud, a process layer switch and intelligent electronic equipment; the virtual connection fault positioning system is used for calculating and generating a virtual connection actual communication link, comparing the virtual connection logic loop with the actual communication link, indicating that the virtual connection of the process layer network is abnormal if the virtual connection logic loop and the actual communication link are inconsistent, and transmitting the fault positioning information to a network monitoring management data cloud; the network monitoring management data cloud is used for storing network operation data and virtual connection fault positioning data to form a fault analysis report. The mapping relation of the process layer network communication virtual connection is vividly displayed in a graphic mode, and the preset process layer network communication virtual connection is compared with the actual process layer network communication virtual connection, so that the real-time monitoring of the process layer network and the fault positioning are realized.