A foundation pit in typical geological condition in mountainous area of Chongqing is analysed as an example. Key points of BIM application in the project is analysed and a three-dimensional modelling flow of foundation pit engineering is proposed. A three-dimensional geology-design coupling model of foundation pit is constructed based on BIM Civil 3D and Revit. Based on this model, the foundation collision check between the main object and the adjacent constructions is tested firstly. Then, three-dimensional display, two-dimensional drawing and statistical computation are established, separately. Finally, the construction process is simulated. The results show that the three-dimensional visualization model based on BIM can realize a fine demonstration of the geological condition and support design, and descript the construction plan dynamically. This model can effectively solve the problems in mountainous city foundation pit engineering, including the uneven distribution of rock and soil, a variety of slope type and retaining structure, adjacent building foundation conflict and the complex construction procedure.