The vibration caused by railways is an environmental constraint in the development of over-track buildings. To study the influence of environmental vibration from the high-speed railway on over-track buildings, a finite element model including track, soil, and buildings was set up. Based on the vertical vibration acceleration sampled on the rail, the equivalent line load acting on rails vertically was obtained by a simplified model. On the basis of verifying the simulation model by measurement results, the vertical vibration induced by high-speed railways in over-track buildings was studied quantitatively. Through introducing correction terms relating to the thickness and height of the over-track platform, the story number, and the structure of the over-track building, an existing model released by the railway industry of China was improved. Compared with the existing model only being suitable for predicting vertical vibration of the first floor, the improved model can predict vertical vibration of different floors.