Stator faults are one of the common issues in pumped storage generators, significantly impacting their performance and safety. To ensure the safe and stable operation of pumped storage generators, a stator fault diagnosis method based on an improved short-time Fourier transform (STFT)-support vector data description (SVDD) hybrid algorithm is proposed. This method establishes a fault model for inter-turn short circuits in the stator windings of pumped storage generators and analyzes the electrical and magnetic states associated with such faults. Based on the three-phase current signals observed during an inter-turn short circuit fault in the stator windings, the three-phase currents are first converted into two-phase currents using the principle of equal magnetic potential. Then, the STFT is applied to transform the time-domain signals of the stator’s two-phase currents into frequency-domain signals, and the resulting fault current spectrum is input into the improved SVDD network for processing. This ultimately outputs the diagnosis result for inter-turn short circuit faults in the stator windings of the pumped storage generator. Experimental results demonstrate that this method can effectively distinguish between normal and faulty states in pumped storage generators, enabling the diagnosis of inter-turn short circuit faults in stator windings with low cross-entropy loss. Through analysis, under small data sample conditions, the accuracy of the proposed method in this paper can be improved by up to 7.2%. In the presence of strong noise interference, the fault diagnosis accuracy of the proposed method remains above 90%, and compared to conventional methods, the fault diagnosis accuracy can be improved by up to 6.9%. This demonstrates that the proposed method possesses excellent noise robustness and small sample learning ability, making it effective in complex, dynamic, and noisy environments.