Ni80Cr20 alloy film shows a good neutral transmission in visible light. The quartz crystal sensor in the coating machine has a system error, which results in the actual thickness being different from the standard value. To solve this problem, a new manufacturing method for controlling film thickness of neutral density filters was proposed in this paper, which is bombarded the membrane surface with low energy ion beams. Make the relative error of optical density value is controlled within ±2%, and the absolute error is not more than ±0.01. The error of the thickness of the film is controlled at the atomic layer scale, which meets the requirements of the use of the filter in the spectral system with high precision. It is verified that the neutral density filter still has good optical properties and surface flatness after ion beam etching in this experiment. The technology of ion beam bombardment etching becomes a new and reliable method to control the thin film thickness.