Noise from rail transit viaducts often has a negative effect on surrounding buildings and nearby residents. To reduce the bridge vibration and radiated noise, floating slab tracks have been widely adopted in rail transit viaducts. To calculate the vibration of coupled track-bridge systems, both time-domain and frequency-domain methods can be applied although their relative performance is not very clear. This study aims to compare the two approaches and then provide some guidelines in choosing the appropriate method for predicting the vibration. The principle and methodology of the two calculation methods are firstly introduced, and the models for the train, floating slab track and bridge are developed using similar parameters. To further improve the efficiency and accuracy of the frequency-domain method, a half period method and a weighted average method are proposed to calculate the average responses of a certain point on the rail, floating slab and bridge to approximate the response during the pass-by. An indirect method is used to estimate the wheel–rail combined roughness from the measured rail acceleration when the train is running on the bridge, and compared with the direct measurement rail roughness. For the vibration of the bridge and floating slab, comparisons are made between results obtained from the time-domain and frequency-domain methods with different train speeds, and between results from experiment and simulation with different roughness. It is found that the wheel–rail contact forces and other structural responses from the two approaches show good consistency in the frequency region above 20 Hz. It is shown that a good approximation of the response during the pass-by can be obtained using the frequency-domain method by adopting the half period average or a simplified weighted average of two wheel position cases. When using the measured roughness and estimated roughness, the simulated vibration of the floating slab and bridge match well with the experimental results, and the indirect method can be used to modify direct measurement roughness in lower frequency regions. In the vibration prediction, the rail vibration or roughness, and other parameters in the vehicle–track–bridge system, should be measured accurately to ensure high reliability.