Abstract: Objective To explore the effect of femtosecond laser-assisted in situ keratomileusis (FS-LASIK) and small incision lenticule extraction (SMILE) femtosecond laser in the treatment of myopic astigmatism with thin cornea. Methods From September 2022 to September 2023, 128 patients with thin cornea myopic astigmatism in the hospital were selected and randomly divided into FS-LASIK group (64 cases, 128 eyes, receiving FS-LASIK) and SMILE group (64 cases, 124 eyes, receiving SMILE). The visual acuity uncorrected visual acuity (UCVA), best corrected visual acuity (BCVA) before surgery and at 1 year after surgery, refractive parameter spherical equivalent (SE) at 3, 6 and 12 months after surgery, corneal surface morphology average corneal curvature (K_Ave), surface regularity index (SRI), surface asymmetry index (SAI) before surgery and at 1 year after surgery, corneal biomechanic indicatorscorneal expansion comprehensive deviation analysis index (BAD-D), corneal biomechanical index (CBI), total biomechanical index (TBI) and corneal injury degree corneal endothelial cell count, corneal endothelial cell size, coefficient of variation (CV) and differences in postoperative astigmatism correction vector indicators magnitude of error (ME), angle of error (AE), correction index (CI), and index of success (IOS) were compared. Residual stromal bed thickness and the incidence of complications after surgery were recorded. Results One year after surgery, both UCVA and BCVA in both groups were improved compared with preoperation (P<0.05), but there were no significant between-group differences (P>0.05). At 3, 6, and 12 months postoperatively, the SE levels in both groups were higher than preoperation (P<0.05); however, there were no statistically significant differences in SE levels between the groups at above time points (P>0.05). One year after surgery, K_Ave, SRI, and SAI in both groups were lower than preoperative levels, and the SMILE group was lower than those in the FS-LASIK group (P<0.05). One year after operation, BAD-D and TBI in both groups were higher than preoperative levels, while CBI was lower than preoperative levels; however, BAD-D and TBI in the SMILE group were lower than those in the FS-LASIK group, and CBI was higher than that in the FS-LASIK group (P<0.05). One year after surgery, corneal endothelial cell counts in both groups were lower than preoperative levels, and CV of corneal endothelial cell size was higher than preoperative levels; however, corneal endothelial cell count in the SMILE group were higher than those in the FS-LASIK group, and the CV of corneal endothelial cell size was lower than that in the FS-LASIK group (P<0.05). There were no statistically significant differences in ME, AE, CI, and IOS between the two groups (P>0.05). The residual stromal bed thickness was (302.01±55.03) μm in the FS-LASIK group and (310.23±46.03) μm in the SMILE group after surgery, with no statistically significant between-group difference (t=1.284, P=0.200). One year after surgery, there were 5 cases of dry eye in the FS-LASIK group and 2 cases in the SMILE group, with no statistically significant difference in incidence of dry eye between the two groups (χ²=1.227, P=0.268). Conclusion For patients with myopic astigmatism with thin cornea, both FS-LASIK and SMILE can achieve satisfactory improvement in visual acuity and refractive state, and the latter one has a relatively small impact on the integrity of corneal structure, biomechanical stability and surgical injury.