The research investigates two kinds basic problems during the precision processing about turbo molecular pump rotor using 5-axis machining center. The one is to study the geometric and dimensional precision of turbo molecular pump rotor. The other one is to study the accuracy evaluative factors of 5-axis turbo molecular pump rotor machining center. For improving the processing precision to ensure the dynamic symmetry and geometric symmetry of the turbo molecular pump rotor, it focus on analyzing the allowable deviations from the turbo molecular pump rotor’s nominal geometry and dimensions specified during the design stage by defining tolerances on the part’s features using geometric dimensioning tolerancing standards and homogeneous transformation matrix. The geometric and dimensional errors deviation model of this feature can be represented by a HTM Hq. From the errors of the machine tools, using rigid body kinematics techniques and HTM, the systemic geometric volumetric error models are established for error synthesis. Volumetric accuracy model can be verified effectiveness better estimation of machine performance, by means of physical simulation and measurement.