The accuracy of machine tools is significantly affected by the geometric defect and thermal deformation of the mechanical components. This paper intends to provide a comprehensive compensation method for the integrated geometric and thermal errors of machine tools. Firstly, a synthesized volumetric model is established with homogeneous transformation matrix method, considering both the geometric and thermal effects. Then, in order to improve the modeling accuracy and efficiency of the geometric error components, an automatic modeling algorithm is proposed with the Chebyshev polynomial-based orthogonal least squares regression. Also, to improve the robustness of the thermal error models for the feed axes and the spindle system, the thermal effects caused by external ambient variation and internal heat sources are identified and modeled separately. Finally, an intelligent virtual compensation system is developed for machine tools based on the function of external machine original coordinate shift and fast Ethernet data interaction technique, and compensation tests on a vertical machining center showed that the position accuracy of the machine tool could be significantly improved after compensation.