The new generation of low-earth-orbit (LEO) satellite constellation systems has the characteristics of low delay, strong signal and global coverage, and it is an important direction for the development of next-generation communication technology. A major disadvantage is that the constellation system is huge, often composed of hundreds or thousands of satellites, which puts forward high requirements for the design and health management of the constellation system, and the existing telemetry data monitoring system cannot meet the actual needs. CPS is a multidimensional complex system that integrates computation, communication and control (3C). Through the deep integration and cooperation of 3C, the real-time monitoring and dynamic control of large-scale engineering systems are realized, which is completely suitable for the operation and maintenance requirements of the satellite constellation system. This paper firstly establishes the entire satellite constellation system model, which is integrated from the satellite multidomain system, the constellation orbit environment system and the communication link system. Then, according to the technical concept of cyber-physical systems (CPS), an implementation framework of a prognostics and health (PHM) system driven by a model–data hybrid for satellite constellation systems is proposed. The framework is based on model simulation data and telemetry data and combines virtual and real data fusion, fault diagnosis, simulation prediction and other technologies to generate enhanced data to drive the effective operation of the PHM system. Finally, a verification case is designed to prove that the satellite constellation health management system implemented under this framework has a positive effect on the reliable operation and maintenance of the satellite constellation system.