A joint prediction method of “mathematical modeling and finite element calculation” is proposed to improve the prediction of machining quality in weak magnetorheological shear thickening fluid polishing of complex surfaces. The study proceeded in several steps. First, based on both impact energy model and material removal model, a numerical prediction model of surface roughness is established. Second, based on the multi-peak fitting method, the field-induced rheological properties of the polishing fluid are characterized and material properties of the flow field medium in the polishing zone are defined. Third, the numerical boundaries of polishing flow velocity and shear stress in the above prediction model are obtained. Fourth, the polishing experiments with parameters consistent with the above simulation model are conducted, and the initial surface roughness values are substituted into the above prediction model. The results show that the joint prediction method can effectively predict the machining quality of workpiece surface. The absolute error of Sa value of surface roughness is up to 10.6 nm, and the maximum relative error is 12.3%.