To comprehensively obtain the effect of the machining process on the three-dimensional surface topography of machined potassium dihydrogen phosphate crystals, a dynamic response model of a machining system was built to calculate the dynamic displacement variables in the different processing directions. This model includes almost all processing factors, such as cutting parameters, environment vibration, radial and axial runout of the spindle, cutting tool parameters, material parameters, guide way error, fast tool servo and lubrication condition errors, etc. Compared with the experimental results, the three-dimensional topographies and two-dimensional profiles of the simulation surfaces were nearly consistent with those of experimental machined surfaces. As the simulation shows, the cutting parameters, axial runout of the spindle, and the output noise of the fast tool servo can respectively impact the main, low, and high frequencies of the machined surface topography. The main frequency of all the simulated and experimental surfaces in this study was 0.0138 μm−1. The low and high frequencies of the simulation surfaces had slight differences, about 0.003 μm−1 from those of the experimental surfaces. The simulation model, based on dynamic response, can accurately predict the entire machining process and three-dimensional topographies of machined potassium dihydrogen phosphate surfaces.