In order to study the mechanism of the profile evolution process, a three-dimensional (3D) profile evolution method based on compression representation is proposed to simulate the plasma etching process and consider emphatically ion etching. To solve the problem of large memory requirements of 3D cellular model, the presented method adopts a new data structure, which combines two-dimensional array with dynamic storage, to represent cellular information. The structure realizes the lossless compression of cellular information and keeps the spatial correlation between 3D cells. The experimental results show that the method not only significantly reduces the memory, but also has a higher searching efficiency of surface cell which ion first passes through in high-resolution simulation. The method is applied to 3D profile evolution simulation of silicon etching process. A comparison between the simulation results and the experimental results also verifies the effectiveness of the proposed method.