Abstract: Since the transient process research of the generator internal short circuit fault is complex because of the asymmetry of the electric structure under the fault condition, the study establish a simplified generator model which is fit for multi-branch generator internal short circuit fault analysis. Based on the model, the study simulates all the possible internal faults of the ALSTOM generator in the Three Gorges Right Bank Power Station, China. Then the study analyzed the protection effects of different protection theory under different connection modes of stator branches on neutral side, and the best main protection configuration scheme is proposed in the end.