Objective To compare the efficacy of femtosecond laser small incision lenticule extraction(SMILE) and femtosecond laser assisted LASIK(FS-LASIK). Methods This is a prospective nonrandom cohort study. There were 200 eyes of 200 cases in both SMILE group and FS-LASIK group respectively. Uncorrected visual acuity(UCVA), best corrected visual acuity(BCVA) and residual refraction (spherical equivalent, SE) were measured before surgery and 3 months after surgery. Vertex altitude of corneal posterior surface and corneal wavefront aberrations were measured by pentacam. Data were compared between two groups and between preoperation and postoperation in same group. Results Difference was not statistically significant in visual acuities, SE, safety, effectiveness and predictability between two groups (P>0.05). Pre-operative and postoperative vertex altitude of corneal posterior surface in SMILE group were(1.96±2.15) μm, and(2.08±1.87)μm, whereas those in FS-LASIK group were(1.96±2.15) μm, and(2.08±1.87)μm, and there were no statistically significant differences between preoperative and postoperative results in both groups (P>0.05). There was no statistically significant difference in postoperative outcome between two groups(t=2.527, P=0.16). Compared with pre-operative results, the corneal aberrations increased after surgeries, including root mean square of total (RMS TOTAL), root mean square of lower-order abberation (RMS LOA), root mean square of higher-order abberation (RMS HOA) and root mean square of spherical abberation (RMS Z4, 0) (P=0.000). Although corneal aberrations in SMILE group were bigger than those in FS-LASIK group, but there were no statistically significant differences between two groups (P>0.05). Conclusion Both SMILE group and FS-LASIK group have good safety, effectiveness and predictability, and corneal posterior surfaces of two groups all keep stable after surgery. Small incision without corneal flap is the most significant advantage of SMILE which can avoid potential risks, such as striation, shift and losing of corneal flap. Key words: Keratomileusis, laser in situ, femtosecond laser assisted(FS-LASIK); Small incision lenticule extraction (SMILE)