To ensure the ride quality of metro system in mountain cities, the characteristics of the wind-train-bridge system with high-piers are studied, and the corresponding safety threshold is calculated in this paper. The improved spatial gust model considering the wind speed-up effect in mountainous terrain and spatial correlation is established. The time series of the wind loads are input to the dynamic system. The finite element method is used to model the bridge and the track, the multi-rigid-body system connected with the suspension spring and the damper is used to model each vehicle in the train. The whole process of the metro train running on the three-span high-pier viaduct is simulated. The study shows that both amplitude and frequency components of fluctuating wind have greater influence than the average wind, which can make the calculation result tend to be conservative and more conducive to analyze the vehicle running performance. Due to the comprehensive effect of the correlation of gust in spatial distribution, different vehicle parameters and aerodynamic coefficient differences, the response of each vehicle is different. The windward side of the high-pier bridge is the conservative calculation condition to evaluate the running performance. The wind barrier weakens the wind resistance of the bridge, but greatly improves the wind environment for the train. Metro train is less sensitive to increased wind speed with the wind barrier, but exceeds the limit under the same condition without any measures. When wind speed reaches 30 and 32 m/s, the ride comfort and running safety cannot be guaranteed respectively. The corresponding value for with single-side and bilateral barrier are 0.063 g and 0.061 g, decrease by 37% and 39% than that without barrier, and the value with two barriers are 0.216 and 0.211, decrease by 73% and 74%.