In biological micromanipulation, cell penetration is a typical procedure that precedes cell injection or oocyte enucleation. During this procedure, cells usually undergo significant deformation, which leads to cell damage. In this paper, we focus on modeling and evaluating the cell penetration process to reduce cell deformation and stress, thereby reducing cell damage. Initially, a finite element model (FEM) is established to simulate the cell penetration process. The effectiveness of the model is then verified through visual detection and comparison of cell deformation with experimental data. Next, various mechanical responses are analyzed, considering the influence of parameters, such as the radius and shape of the injection micropipettes, material properties, and size of the cells. Finally, the relationship between the intracellular stress and the cell penetration depth of biological cells is obtained. The evaluation results will be applied to develop optimized operation plans, enhancing the efficiency and safety of the cell penetration process.