The invention provides a method of fault location for a communication link in an intelligent substation process layer. The method comprises the following steps of analyzing an SCD file, obtaining a GOOSE / SV virtual loop information, and acquiring information of a sending terminal device, a receiving terminal board and ports; analyzing an SPCD file, obtaining process layer network information, and forming a set of each path Path; analyzing reported broken chain alarm information, receiving a sending terminal board card and ports of a virtual loop, ports between a sending terminal and a receiving end and a path set through the information of the sending terminal device, the receiving terminal board, the ports and the Path set in the network topological structure; calculating port fault probabilities with the combination of the device current communication state; and checking corresponding devices according to the fault probabilities from high to low. The method can rapidly position the communication fault point in a simple, reliable and effective manner, and ensure the reliable operation of the secondary circuit.