System-Theoretic Process Analysis (STPA) was extended with formal method. In the extension, the extended UML model of the system was established and transformed into PHAVer model. The formal definition and the structure of fault model were also proposed, with which the fault model of the system was set up. Then, the PHAVer model and the fault model were integrated into one PHAVer model which included all the faults. Based on this integrated model, factors causing inadequate control were identified with the reachable set analysis, which performed the safety analysis of the system. Taking radio block center handover of CTCS-3 level system for example, STPA merging with formal method was taken for analyzing the given hazard. The result shows that the proposed method is suitable for the functional safety analysis of CTCS-3 level system.