X-ray free-electron lasers are large modern scientific devices that play an important role in fields such as frontier physics and biomedicine. In this study, a light source is connected to an experimental station through beam lines, which requires numerous ultra-smooth and high-precision X-ray mirrors. Monocrystalline silicon is an ideal substrate material where ion-beam figuring is required. However, the ultra-smooth surface is damaged after the ion-beam figuring. Through an analysis of the machined surface, it is found that in the process of vacuum pumping, the impurities in the cavity adhere to the machined surface and increase the roughness after processing. Therefore, an optimized vacuum-pumping scheme is proposed. The experiment demonstrates that the original value of the processed surface roughness remains unchanged.