Thin copper substrates in precision physical experiments are commonly machined by double-sided lapping to obtain high flatness. However, the flatness is limited by the accuracy of lapping plate, process vibration and so on in double-sided lapping process. Hence, magnetorheological finishing (MRF) with its good performance on profile modification is employed to improve the flatness. Nevertheless, thin copper substrates, which are sensitive to the stress, deformed easily with uneven material removal on the surface. In this paper, MRF is conducted on machining thin copper substrate for the first time considering deformation induced by stress. A finite element model is established to evaluate the deformation by residual stress, and the results show that the deformation tends to be more serious with the increase of the material removal. According to the simulation results, the material removal is optimized considering both deformation and efficiency, and a series of experiments are conducted on a Φ100×2.8 mm workpiece to verify the simulation results. The experimental results show that the flatness is further improved from peak to valley (PV) 6.6 μm to PV 2.3 μm with optimized processing parameters. Hence, the feasibility of magnetorheological finishing on thin copper substrate is demonstrated.