A numerical model was established by the level set method to simulate the etching profile evolution in HgCdTe ion beam etching. The input parameters are: mask thickness, the slope of mask sidewall, trench width, ion angular distributions, etching speed, et al. Etching lag and etching profile of HgCdTe were simulated and compared with the experimental results. The results show that, given nominal trench width 4~10 μm, the errors between simulated etch depths and that of the experiments are 6~20%. The profile evolution of etching mask was simulated and an example was given to illustrate how to design the mask thickness to improve the aspect ratio.