Cyber physical systems (CPSs) are integrations of computation and physical processes. As a complex hybrid system, the reliability of CPSs is very important. Some work on the reliability of CPSs has been done, but most of them just present abstract ideas or models based on single component. In this paper, we use a phased-mission system (PMS) model to analyze the reliability of CPSs. The model consists of Markov models for components, and a binary decision diagram (BDD) for the system structure function. Moreover, a CPSs architecture model of an aircraft fuel management system (AFMS) is also presented. At last, we compute the reliability of a specific AFMS based on the PMS model.