The high-speed motorized spindle is the core component of the machine tool, and its assembly accuracy directly determines the quality of the processing product and the service life of the spindle itself. As a typical revolving components assembly, it is critical to ensure that the radial and axial runout performance of the assembly is extremely excellent to satisfy the requirements of high precision and rigidity. Meanwhile, geometric deviations are inevitably observable on manufactured components of spindle, especially the form deviations of revolving part have huge influences on the quality and function of spindle. However, geometric deviations are reduced to dimensional and orientation defects without considering form deviations in most previous models of deviation analysis. Skin Model Shape of a work piece is a discrete geometry representation of the physical interface between the work piece and its environment, which is based on a representation of non-ideal work pieces employing discrete geometry representation schemes. This paper presents a deviation analysis method for high-speed motorized spindle assembly using Skin Model Shapes, concerning all kinds of geometric deviations of the components. Deviations of the components are represented by the Skin Model Shapes, which is a point cloud-based discrete representative that is able to model the actual toleranced surfaces instead of the ideal or associated ones in an assembly. This paper solves the constrained objective function by means of the ideas of sequential quadratically constrained quadratic programming (SQCQP) method, which can solve problems with high degree of non-linearity and also has relatively small amount of calculation. The procedures outlined in the paper are quite general and can be used for tolerance analysis of any assembly process.