Compared with federated avionic architecture, the integrated modular avionic (IMA) system architecture in the aircraft can provide more sophisticated and powerful avionic functionality, and meanwhile, it becomes structurally dynamic, variably interconnected, and highly complex. The traditional approach such as fault tree analysis (FTA) becomes neither convenient nor sufficient in making safety analysis of the IMA system. In order to overcome the limitations, the approach that FTA combines with generalized stochastic petri net (GSPN) is proposed. First, FTA is used to establish the static model for the top level of the IMA system, while GSPN is used to build a dynamic model for each cell system. Finally, the combination model is generated, which is called the FTGPN model. Moreover, the FTGPN model is made safety analysis with the PIPE2 tool. According to the simulation result, corresponding measures are taken to meet the safety requirements of the IMA system.