The existing fault diagnosis methods for 3/2 connection system take little account of dead-zone fault, which can easily lead to misdiagnosis based on the alarm information of protection and circuit breaker. A fault diagnosis method of 3/2 connection substation based on Petri nets is proposed with dead-zone fault taken into account. Temporal weighted fuzzy Petri net model is constructed for dead zone besides the bus, line, and transformer. According to the tripping strategies of different types of dead-zone faults in different positions, identification logic for dead-zone fault is proposed with information of protection action and circuit breaker’s opening and closing state. Thus the structure and parameters of diagnosis model can be modified by identifying the dead-zone fault logic and checking the timing constraints of the protection and circuit breakers. Simulation results of testing system and actual fault cases of power grid show that this method can accurately identify the fault component in complicated condition of alarm information incompleteness and maloperation or rejection of protection and circuit breaker, which improves the accuracy and fault-tolerance of the diagnosis. This work is supported by National Natural Science Foundation of China (No. 51277084 and No. 50877031).