With the continuous development of modern optical systems, the demand for full spatial frequency errors of optical components in the system is increasing. Although computer-controlled sub-aperture polishing technology can quickly correct low-frequency errors, this technology significantly worsens the mid-frequency errors on the surface of the component, which greatly inhibits the improvement of optical system performance. Therefore, we conducted in-depth research on the non-stationary effect of the removal function caused by the fluctuation in magnetorheological polishing and their influence on the mid-frequency errors of the component surface. We established a non-stationary profile model of the removal function and applied this model to simulate the distribution of mid-frequency errors on the surface of the processed component, considering the non-stationary effect. The simulation results showed that the non-stationary effect of the removal function weaken the mid-frequency ripple errors but increase other mid-frequency errors. Therefore, we first proposed the optimal single-material removal thickness corresponding to the non-stationary effect and experimentally verified the effectiveness of the optimal material removal thickness in suppressing mid-frequency errors. The experimental results showed that when the magnetorheological finishing single-material removal thickness is set to the optimal value, both the mid-frequency ripple errors and the mid-frequency RMS on the surface significantly decrease. Therefore, this work provides a basis for improving the existing magnetorheological finishing process and effectively suppressing the mid-frequency errors on the surface of processed components. It also provides theoretical and technical support for the magnetorheological processing and manufacturing of high-precision optical components. At the same time, the non-stationary effect and the corresponding analytical models has the potential to be extended to other polishing tools.