Frequency response analysis (FRA) is a popular tool to detect transformer winding deformation faults. It has been recently used to diagnose the winding inter-turn short circuit fault of the electric machine. The application of FRA is based on the fact that the winding can be equivalent to an electrical circuit consisting of resistance, inductance, and capacitance. Therefore, to obtain an accurate broadband equivalent circuit model of synchronous machine and perform the fault analysis and diagnosis, this paper introduces the gray box model technique based on the state space and genetic algorithm. The electrical circuit of a form-wound coil of a 4 kW machine with known electrical parameters is used to verify the proposed method primarily. Besides, the equivalent circuit modeling is carried out and experimentally verified on an actual 5 kW synchronous machine. Finally, the fault simulation analyses of winding inter-turn short circuits are performed based on the proposed equivalent electrical circuit. The verification result shows that the circuit parameters identified by the proposed method are accurate. Moreover, the fault simulation results indicate that the inter-turn short circuit faults can cause apparent variations in the frequency response curves. It is feasible to detect the winding fault of the synchronous machine by the FRA method.