Objective To establish a finite element simulation system for the surgery of small incision lenticule extraction (SMILE) and provide foundation for the optimization of SMILE based on simulation results of corneal biomechanical properties, and to study the effect of corneal collagen cross-linking ( CXL) on biomechanical properties of the cornea after SMILE. Methods The mechanical behaviors of the cornea were characterized by hyperelastic constitutive relations with the consideration of gradient distributions of cross-linking strength. The indentation finite element model of SMILE was established. By setting up different surgical parameters such as incision position, incision length, side-cut angle and thickness of corneal cap, the corneal biomechanical behaviors after SMILE were simulated and analyzed. The finite element simulation under different irradiation doses was conducted to analyze the effect of CXL on the cornea after SMILE. Results The maximum von Mises stress increased as the angle of incision position decreased, the incision length increased, the side-cut angle changed from 90° to 135° or 45°, and the thickness of corneal cap decreased. Moreover, the maximum von Mises stress after CXL increased with the radiation dose increasing. Conclusions The finite element model of SMILE constructed in this study can effectively be used to characterize corneal biomechanical responses and provide simulation references for the optimization of SMILE. In addition, the reduced corneal biomechanical strength after SMILE can be effectively improved by CXL.