The 3D clearance of a high-speed train (HST) is critical to ensure the safety of railway transportation. Many studies have been conducted on the inspection of the clearance profile in railway operation based on the vision system, but few researchers have focused on the computation of the 3D clearance in the design phase of an HST. This paper summarizes the virtual 3D clearance computation of an HST based on model integration and the convex hull method. First, both the aerodynamic and kinetic analysis models of the HST are constructed. The two models are then integrated according to the corresponding relationship map, and an array of transformation matrixes of the HST is created to drive the designed model simulating the physical railway motion. Furthermore, the convex hull method is adopted to compute the 3D envelope of the moving train. Finally, the Hausdorff metric is involved in the measurement of the minimum clearance model and the 3D envelope model. In addition, the color map of the Hausdorff distance is established to verify that the designed shape of the HST meets the national standards. This paper provides an effective method to accurately calculate the 3D clearance for the shape design of an HST, which greatly reduces the development cost by minimizing the physical prototype that must be built.