Objective To establish a finite element simulation system for the surgery of SMILE and provide foundation for the optimization of SMILE based on the simulation results of corneal biomechanical properties, and to study the effect of corneal cross-linking (CXL) on the biomechanical properties of the cornea after SMILE. Method The mechanical behaviors of cornea before and after the surgery were characterized by the hyperelastic constitutive relations with the consideration of gradient distribution of the crosslinking strength. The indentation finite element model of SMILE was established with the Abaqus software. 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. Result The maximum value of 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 value of Mises stress after CXL increased with the radiation dose. Conclusion The finite element model of SMILE constructed in this study could effectively be used to characterize the corneal biomechanical properties and provide the simulation reference for the optimization of SMILE. In addition, the reduced corneal biomechanical strength after SMILE could be effectively improved by CXL.