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Aiming at the problems of modeling for electric power systems with main protection and back-up protection, a fault tree analysis method was proposed through modeling the core fault. This model shows happening and formation of failure clearly, but fault tree suffers limited and hindering with the problem of NP. It also has low efficiency when traversing and searching. So changing fault tree model to Petri net model which can use state transition equation conduct matrix operation, Quickly and accurately diagnosed failure element, reduce the complexity of the diagnosis. An example of electric power systems provided to demonstrate the diagnosis method which simple and effective.