To meet the requirement of high reliability and indemnificatory to power supply system of certain weapon system，the general structure of prognostics and health management(PHM) of frequency converter system based on its fault mechanism is presented，the function of every layer in PHM of frequency converter system is explored，and the key technology of PHM system is studied. By considering the rapid calculation requirement, PHM and database of maintenance based on industry personal computer are designed. Intelligent diagnosis algorithm and effective fault prognostics based on the Hilbert transform technology are proposed. The correctness and validity of the structure of PHM of frequency converter system are tested and verified though the experiments. The system fulfils the basic functions of prognostics and health management for frequency converter system. It provides an effective method of prognostics and protection for typical frequency converter system.