The large-scale variable-speed pumped storage unit has the characteristics of alternating current excitation and variable-speed constant-frequency power generation. It is of practical significance to study the internal fault simulation to clarify the optimal configuration scheme of its main protection. First, a general mathematical calculation model of a variable-speed pumped storage power generation motor is established based on the branch voltage equation and flux linkage equation. This can realize the transient simulation of the internal short-circuit fault and the open-welding line fault of the stator winding under grid-connected full load condition. The fault characteristics of the two types of faults in the simulation results are consistent with the theoretical analysis, and this verifies the correctness of the mathematical calculation model. Then, all possible short-circuit faults and disconnection faults are analyzed according to the winding law of the stator winding, and the established mathematical model is used to simulate and calculate all faults. Finally, it is found that the protection coverage is the best when the main protection configuration scheme is ‘zero sequence transverse and split phase transverse and complete longitudinal differential current protection’ through quantitative analysis and comparison. This work is supported by the National Natural Science Foundation of China (No. 51877089).