According to the actual situation of train operation, track and subgrade are regarded as a part of the vibration structure of vehicle model, a secondary suspension vertical coupled dynamic model including vehicle, rail, sleeper, ballast, subgrade and foundation has been established. The effect of train speed on vehicle operation quality, dynamic displacement and subgrade dynamic stress is analyzed. The results show that the vehicle acceleration, the dynamic wheel load and offload factors increase with train speed, and distribute linearly. The safety of train operation and running comfort can meet the requirements when the high-speed train under secondary suspension passing through ballasted track subgrade structure. The dynamic displacement of the system is less influenced by train speed. The dynamic stress of subgrade surface increases with speed improving, and it is distributed as saddle along the lateral direction and as parabola a-long the longitudinal direction of subgrade surface. The dynamic stress of subgrade declines sharply along the depth of subgrade. The dynamic stress on 3 m depth below subgrade bed surface is about 16 percent of that of subgrade surface. Results of this study agree well with some existing document results, which shows that the model is of high reliability.