With the continuous construction of high-speed railway tunnels, proper seismic performance indicator for high-speed railway tunnels concerning the train operation safety is urgently needed. To establish such indicator, a coupled vehicle-track-tunnel refined finite element model is developed through the joint simulation of HyperMesh and ABAQUS, in which the interaction between the subsystems and influence of uneven stratum are thoroughly considered. The model is further validated by comparing the numerical results with theoretical solution and measured data. Significant impact of soil layer heterogeneity is also illustrated, indicating the necessity of complex stratum modeling. Based on the refined finite element model, dynamic simulation of the vehicle-track-tunnel coupling system under seismic excitation is performed, and a two-level seismic performance indicator for high-speed railway tunnel is established, which offers a quantitative evaluation approach for seismic design. Though the established seismic performance indicator is proved effective in certain circumstances, further verification and refinement is still required in future research.