It is necessary to analyze scenarios in which several failures are occurred at the same time for improving signal system security analysis efficiency. Since the existing finite automaton could not solve above problems, a hybrid modeling method for signal system security analysis was designed. In a certain scenario, the finite automaton model was used to analyze the security risk of a certain failure, at the same time, Petri nets modeling method was used for security risks analysis of scenarios in which several failures occurred and were characterized with asynchronism and concurrency. The relevant parameters and performance indexes of specific scenarios were determined by the modeling method, and the signal system security analysis simulator of all modeling scenarios were achieved by using software tools (VC6.0). The system security analysis was carried out orderly and effectively by using the developed simulator for reducing human experience error, improving the efficiency of signal system security analysis, and avoiding the important security risks.