This paper proposed a hierarchical model for smart substation fault diagnosis. This fault diagnosis system gets fault information from SCADA and fault information system. The information from SCADA, including network topology and switch state, is modeled based on IEC61970-CIM. The protection information from the fault information system is modelled based on IEC61850, then encapsulated CIM model. When a fault happens, the component connecting topology trees were used for creating the Petri Nets model of possible fault components. Finally according Petri Nets model the true fault primary devices were identified, and the false tripping or operating information were picked out. This fault diagnosis model standardized the fault information and can share fault diagnosis results with other systems, realized real-time online fault diagnosis of power systems.