A simulation method is used to optimize the residence time distribution and modification process. The beam shape of the ion beam is changed by adding an diaphragm at the light exit of the ion source. Ion beams with different apertures are simulated on MATLAB software and the ion beam is modified according to different stacking intervals. In the simulation process, we introduce a correction method to obtain the residence time distribution and residual distribution of the surface shape remaining after the removal of material. We analyze the removal rules to determine the best aperture size, stacking interval, and residencetime distribution. The initial peak and valley value of the fused silica plane is 1079.59 nm, the root mean square value is 304.95 nm, and the diameter is 120 mm. The shape is modified on the basis of simulation. We modify the surface shape on the basis of the simulations. After 13 h of modification, the peak-to-valley accuracy of the surface profile is improved to 95.62 nm, RMS value is improved to 8.99 nm, and RMS value of the convergence ratio of the surface profile is 33.92.