Aimed at the requirement of digital precision analysis and tolerance design for the machine tool system, a method of computer aided tolerance analysis and design was proposed. Based on defining the system-oriented tolerance semantics on geometry element, tolerance mathematical models of several basic geometry surfaces were inferred. The restrictions of geometry surface on 6-DOF were included in the model, and were expressed in the form of homogeneous coordinates transformation matrix, so as to be easily compatible to the error model of machine tool. The demonstrations about forecasting method of tolerance control effect are given finally.