Based on the Z-map model of a workpiece and the dynamic cutting forces model of peripheral milling in which the regenerative effect of tool radial runout and axial drift are considered, a model for the prediction of surface topography in peripheral milling operations is presented. According to the stability lobe diagram obtained by the zero-order analytical method, the relationship between spindle speed and surface topography, the tool radial runout, and the axial drift following the chatter are studied. The results show that a stable cutting status but a poor surface finish is obtained at the spindle speeds at which the dominant frequency of the milling system is integral multiples of the selected machining frequency, and a stable cutting status with a good surface finish can be obtained near and on the left side of the resonant spindle speeds determined by the predicted stability lobe diagram. The motion equations of any tooth end mill for peripheral milling are established, and these equations are based on the transformation matrix and the vector operation principle of motion-homogeneous coordinates. In addition, the simulation algorithm and the system of surface topography generated in peripheral milling are given based on the Z-map model. Cutting tests are carried out, and good agreement between the measured surface topographies and the topographies predicted by the model in this study is found in terms of their shape, magnitude, feed mark, profile height of cross-section, and surface roughness. The simulation results show that the milling surface roughness increases with the increase in feed per tooth, which further shows that this simulation system has high credibility. Thus, the simulation and experimental results can provide some practical instructions for the actual peripheral milling in determining the optimal machining conditions.