The positions of geometric elements were represented by three-dimensional correlation coordinates based on probabilistic statistics. The theoretical tolerance design model of the rigid shell throwing mechanism was established by analyzing the geometric parameters transfer and accumulation path and using error association operations such as cascade, coordinate transformation, and synthesis. The optimization objective was the sum of the maximum volume and area of the confidence regions for each positional coordinate. The optimization variables were the relevant geometric parameters and their standard deviation. According to the theoretical tolerance optimization results, the tolerance optimization method considering the actual machining error was proposed for the geometric parameters of the parts with a small process capability index and high machining accuracy in the actual machining process, and the design results are compared and analyzed by using the traditional dimensional chain analysis method. The proposed method organically combines the tolerance theoretical model and geometric parameter measurement data, which can effectively improve the qualification rate of assembly precision.