A methodology of the general design of propulsion and power supply (PPS) System in high speed Maglev engineering project is concluded in this paper. The methodology is derived from the experience that accumulated in the operation and maintenance work in the Shanghai Maglev Demonstration Line and the feasibility research of some possible engineering projects, such as Shanghai-Hangzhou Project and Shanghai Maglev Airport Link Project. Then an assistant design tool, MaglevPDS, based on the methodology mentioned above, is introduced. Finally, the design results of MaglevPDS for Shanghai-Hangzhou Project are presented as an example for the application of MaglevPDS.