Due to the large carrying capacity, high efficiency and punctuality, safety and environmental friendliness, rail transit has become the main choice for transportation. However, the traffic-induced environmental vibration and the associated problems becomes an important issue. Therefore, an efficient and accurate environmental vibration analysis tool is required especially for complex transportation systems. This paper proposes a highly efficient and accurate dynamic stiffness (DS) method to analyze the environmental vibration caused by train-track-bridge system. Firstly, a vehicle-track coupling model was built by the software Simpack to obtain the moving load on the track during the train operation. Then, the dynamic stiffness formulations for both the out-of-plane and in-plane vibrations of plates are developed which exactly satisfied the governing differential equations within the whole frequency range. Consequently, the analytical DS model of a bridge is established by assembling the plate DS elements. The Wittrick-Williams algorithm is applied for modal analysis of the bridge. The time-domain moving excitations exerted on the rails are transform into the frequency domain by using the fast Fourier transformation, then the frequency domain responses of the moving load of the bridge is computed by using the dynamic stiffness matrix in frequency domain. Finally, the time-domain responses are recovered by using the inverse Fourier transform. It is demonstrated that the method presented in this paper has significant advantages in both accuracy and efficiency over the commercial finite element method. This research, with further development made by the group, aims to provide a powerful tool for efficient and accurate analysis of environmental vibration in the railway transportation systems.