In general, high-speed machines should be designed to satisfy electromagnetic and mechanical characteristics. In this study, the design of high-speed permanent magnet synchronous generator with two different shaft materials considering overhang effect and mechanical characteristics was performed. It was confirmed that the leakage magnetic flux generated by the two shaft materials electromagnetically affects the high-speed generator. Additionally, it is important to accurately predict the natural frequency mode and critical speed to prevent damage and vibration of the rotating body owing to scattering during high-speed rotation. Therefore, the mechanical characteristics of the designed model were analyzed. In this study, we propose a design method that considers both the electromagnetic effects and mechanical characteristics. Subsequently, verification was performed through experiments and comparisons for the validity and reliability of the proposed design method.