The rail transit vehicle system is an important subsystem with the most frequent operation accidents and the most direct impact on passengers. Based on the particularity of the vehicle system and the complexity of the system, the hierarchical analysis method (AHP) is used to evaluate its safety. High-order judgment matrix often has inconsistency, and the judgment matrix consistency guarantee is the key to the hierarchical analysis method applied. Based on the hierarchical analysis principle, this paper corrects the inconsistency judgment matrix and realizes the optimization calculation based on the genetic algorithm. This paper constructs a vehicle system safety evaluation index system including 26 indexes at three layers and uses the fuzzy comprehensive evaluation method to evaluate the system safety level. The results show that the calculation results based on the improved AHP-GA are significantly better than that based on the conventional AHP method. The comprehensive evaluation conclusion of the case is "average", and the safety level of the vehicle system of the case enterprise needs to be strengthened.