Femtosecond laser small incision lenticule extraction (SMILE) with different residual stromal thicknesses (RST) is set to investigate its effect on corneal biomechanical properties of rabbits in vivo. In this study, 24 healthy adult Japanese rabbits were randomly divided into group A and B. The RST of group A was set 30% of the corneal central thickness (CCT), and the RST of group B was 50% of the CCT. The thickness of the corneal cap in both groups was set one third of CCT. Corneal visualization Scheimpflug technology (Corvis ST) and Pentacam three-dimensional anterior segment analyzer were used to determine corneal biomechanical and morphological parameters before surgery, and 1 week, 1 month and 3 months after surgery. Pearson correlation analysis was used to analyze factors affecting corneal biomechanical parameters after SMILE. The results showed that the corneal stiffness of group A was significantly higher than that of group B at 1 week and 1 month after surgery, and most biomechanical parameters returned to preoperative levels at 3 months postoperatively. The results of correlation analysis showed that postoperative CCT and RST were the main factors affecting corneal biomechanical parameters after SMILE. There was no significant difference in corneal posterior surface height (PE) between 3 months after surgery and before surgery in both two groups. It indicates that although the ability to resist deformation of cornea decreases in SMILE with thicker corneal cap and less RST, there is no tendency to keratoconus, which may be related to the preservation of more anterior stromal layer.