Excessive underground train-induced vibration becomes a serious environmental problem in cities. To investigate the vibration transfer from an underground train to a building nearby, an explicit-integration time-domain, three-dimensional finite element model is developed. The underground train, track, tunnel, soil layers and a typical multi-story building nearby are all fully coupled in this model. The complex geometries involving the track components and the building are all modelled in detail, which makes the simulation of vibration transfer more realistic from the underground train to the building. The model is validated with in-situ tests data and good agreements have been achieved between the numerical results and the experimental results both in time domain and frequency domain. The proposed model is applied to investigate the vibration transfer along the floors in the building and the influences of the soil stiffness on the vibration characteristics of the track-tunnel-soil-building system. It is found that the building vibration induced by an underground train is dominant at the frequency determined by the P2 resonance and influenced by the vibration modes of the building. The vertical vibration in the building decreases in a fluctuant pattern from the foundation to the top floor due to loss of high frequency contents and local modes. The vibration levels in different rooms at a same floor can be different due to the different local stiffness. A room with larger space thus smaller local stiffness usually has higher vibration level. Softer soil layers make the tunnel lining and the building have more low frequency vibration. The influence of the soil stiffness on the amplification scale along the floors of the building is found to be nonlinear and frequency-dependent, which needs to be further investigated.