Aiming at evaluating the SEE performance of complex electronic system, the multi-signal flow graph (MSFG) method is adopted. Based on the theory of the MSFG, the SEE soft error propagation model is proposed, and an analysis methodology is stated. For complex electronic system which consists of VLSIs devices, such as SRAM-based FPGA, the MSFG model has been established and simulated in TEAMS software. The fault diagnosis and the average first failure time are estimated. The report indicates that the percentage fault detection is 100%, and the average first failure time of the system varies from 142.4 hours to 4116.7 days.