The digital value inputs and the trip command outputs of smart substation secondary system depend on the highly reliable operation of GOOSE circuits, of which the on-line monitoring and fault diagnosis are important functions of smart substation. Aiming at the fault diagnosis for GOOSE circuits interruption of smart substation, this paper proposes a fault diagnosis method for GOOSE circuits of smart substation based on Petri net, which accurately locate the fault points by model calculation. In this paper, according to GOOSE circuits of smart substation with the feature of decoupling in bays, GOOSE circuits of line bay and GOOSE circuits of busbar bay are chosen as study representatives to establish Petri net models. Finally, two scenarios, including a GOOSE interruption of the intelligent terminal as well as the line protection and busbar measurement and control device in a line bay, are studied in this paper, which can precisely locate faults and verify the effectiveness of proposed Petri net model of GOOSE circuits.