In view of the disadvantages of low efficiency，low precision，and difficulty in application of the 3D geological model in the port and waterway engineering design，we realize the quick establishment of geological layer model and 3D geological model according to the geological interpolation calculation by the secondary development of Civil 3D. We also realize the arbitrary cutting of the 3D geological model，the generation of the geological profile，and the application of the geological model in the calculation of pile foundation bearing capacity. The engineering practice verifies that this technical method is practical and feasible，which can provide reference for similar application of BIM technology in port and waterway projects.