The long-span bridge consisting of separated box steel girders is prone to vertical vortex-induced vibration (VIV) within the operating a wind speed range of the train. Based on the wind-train-track-bridge (WTTB) dynamic model, this study presents an analysis method considering VIV effects and investigates the effects of vertical VIVs on the dynamic responses of the train-track-bridge system under crosswinds. It is found that the vertical VIV mainly affects the derailment factor, the offload factor, the vertical car-body acceleration, the vertical car-body Sperling index, and the vertical acceleration of bridge decks, and has less impact on other indexes. The vertical dynamic response of vehicles and bridges increases with the vertical VIV modal order, amplitude and frequency. Furthermore, the impact of the high-order vertical VIV modal is outstandingly more significant than that of the low-order vertical VIV modal.