This paper presents an integrated system used for ultra-precision machine tool (UPMT) design in conceptual and fundamental design stage. This system is based on the dynamic, thermodynamic, and error budget theories. The candidate configurations of the machine tool are first selected from the configuration library or a novel configuration designed by the user, according to the functions of the machine tool expected to realize. Then, the appropriate configuration is given by comparing the stiffness chain, dynamic performance, thermal performance, and the error budget of each candidate configuration. Consequently, the integrated design system enables the conceptual and fundamental of the UPMT to be designed efficiently with a theoretical foundation. The proposed system was used for several UPMT designs, which demonstrate the effectiveness of the integrated design system.