Surface quality and accuracy are the main factors which affect the performance and life cycle of the products. Due to the complexity of the machining process, it is difficult to evaluate the machined surface real time. Simulation of the machining process became the main method to predict and control the quality of the machined surface. This article developed a multi-scale simulation system to predict the overall geometrical features of the milled surface. The effects of locating errors, geometrical errors of the machine tool and tool deflections on the quality of the machined surface are included in the proposed model. Also, different strategies are employed to evaluate the macro-scale and micro-scale geometrical deviations of the machined surface to balance the time cost and accuracy. In comparison with the traditional method, both the form deviations and roughness feature of the machined surface can be predicted. Since the static and dynamic properties of the machining system were considered, both the stable and unstable cutting conditions can be analyzed by using the proposed method. At the end of this article, case studies are carried out to validate the proposed method. The effects of the locating errors, geometrical errors of the machine tool and cutting parameters on the quality of the machined surface are analyzed. The significance of their influences on the quality of the machined surface was investigated.