Communication-based train control (CBTC) are automated train control systems using information communication technologies to ensure the safe operation of rail vehicles. With the development of information technology, massive commercial software, hardware products and standard communication equipment are applied to urban rail transit systems, which introduces a crowd of security threats to CBTC systems. This paper proposes a generalized stochastic Petri net model to simulate dynamic interaction between the attacker and defender to evaluate the security of CBTC systems. According to the characteristics of the system and attack-defense methods, we divide our model to the penetration phase and the disruption phase. In each phase, we provide effective means of attack and corresponding defensive measures, and the system state is determined correspondingly. The model parameters are obtained by conducting attack and defense exercises on the semi-physical simulation platform. The system transition probability is derived with the model parameter and the Nash equilibrium of the game between the attacker and defender. The system availability is obtained by calculating the steady probability of each state which can be derived from the GSPN model solution. Our analytic results reveal the seriousness of the system security situation and the significance of defensive measures for system security.