Rotor winding short circuit faults are common faults for variable-speed pumped-storage generator-motors (VSPSGM). At present, the exciting rotor fault protection of VSPSGM is simple and has low sensitivity. It can only act when the instantaneous value of the rotor phase current reaches three times the rated current. Therefore, it is difficult to cover some rotor winding short-circuit faults with weak fault characteristics. It is urgent to study a novel rotor winding short-circuit-fault protection method for VSPSGM. In this paper, a protection method that combines the stator and rotor currents with different frequencies is proposed. The characteristics of the stator and rotor currents before and after the fault is analyzed by using Clark transformation. On this basis, a specific protection criterion is constructed based on the discrete integral operation, which is easy to implement and not affected by the change of rotor speed. Then, the calculation method of the protection setting is proposed, considering the effect of unbalanced voltage and sensor measurement error. Simulation results show that the proposed method can reliably realize the protection of rotor winding faults. It has faster protection action speed than other methods in the same field. The protection coverage rate is over 90%.