Due to the rugged terrain, metro lines in mountain city across numerous wide rivers and deep valleys, resulting in instability of high-pier bridge and insecurity of metro train under crosswind. Compared with the conditions of no-wind, crosswind triggers severer vibration of the dynamic system; compared with the short-pier viaduct, the high-pier viaduct has worse stability under crosswind. For these reasons, the running safety of the metro vehicle traveling on a high-pier viaduct under crosswind is analyzed to ensure the safe operation in metro lines in mountain cities. In this paper, a dynamic model of the metro vehicle-track-bridge system under crosswind is established, in which crosswind loads model considering the condition of wind zone are built. After that, the evaluation indices and the calculation parameters have been selected, moreover, the basic characteristics of the dynamic system with high-pier under crosswind are analyzed. On this basis, the response varies with vehicle speed and wind speed are calculated, then the corresponding safety zone is determined. The results indicate that, crosswind triggers drastic vibration to the metro vehicle and high-pier viaduct, which in turn causes running instability of the vehicle. The corresponding safety zone for metro vehicle traveling on the high-pier is proposed, and the metro traffic on the high-pier bridge under crosswind should not exceed the corresponding limited vehicle speed to ensure the running safety.