The accuracy of machining can be predicted during the design process of CNC machine tools, while the prediction accuracy depends on the prediction model. However, when establishing the prediction model, the coupling effect among the machine tool’s different components is always ignored for modeling efficiency, so this will lead to its reliability cannot be guaranteed. To address this problem, the model reduction theory and the lumped parameter method are used in this study to set the state-space equations of the essential structural parts. Moreover, the electro-mechanical coupling parameter equation of the servo system is transformed into a state-space equation. Then the state-space equations of the components and the servo system are coupled to establish the machine tool dynamic model. Furthermore, a theoretical model of instantaneous undeformed chip thickness is found, and according to the linear relationship between the micro-cutting force and the instantaneous undeformed chip thickness, the instantaneous cutting force model of the cylindrical milling cutter is established. Based on these, the integrated model, which considers the mechanical structure, control system and cutting force, is obtained and further used in Simulink to build the machining accuracy prediction platform, as well as the accuracy of the integrated prediction model is verified. Moreover, the prediction model established by the integrated modeling method can effectively simulate the actual machining conditions of the machine tool, and the superiority of prediction is confirmed by comparing the simulated and measured results in peripheral milling applications. The results show the error in the system response efficiency is 14.8%, while the error in position accuracy and delay characteristics is less than 10%, the error between the predicted size of the prediction model and the actual size is within 28 μm, a minimum prediction error is 7 μm.