With the continuous development of prognostics and health management (PHM) technology, it has been widely applied in satellite, and gradually developed into two directions: on-board PHM and on-ground PHM. For the high health management of the navigation satellite, we proposed and implemented a new on-ground PHM system. We further constructed a health assessment system from four aspects: the fault diagnosis, performance assessment, trend prognostic and life prediction. Subsequently, the health maintenance scheme is recommended based on the health assessment results. The system has been applied in the in-orbit management of navigation satellites, ensuring the healthy and stable service of all satellites, and 13 satellites have been in service beyond their lifetime. The successful application can provide reference for the promotion of navigation constellation health management.