Objective: To compare the effective optical zone (EOZ) and the changes in corneal high order aberrations (HOAs) after small incision lenticule extraction (SMILE) with those after femtosecond laser-assisted in situ keratomileuses (FS-LASIK). Methods: This study included 80 subjects who underwent laser refractive surgery at the Second People’s Hospital of Foshan between February 2019 and May 2020. Only data from the right eye of each subject were analyzed. A total of 43 eyes underwent SMILE while 37 eyes received FS-LASIK. The eyes were further stratified into subgroups based on different programmed optical zones: the 6.5 mm group and the 6.0 mm group. EOZ, coma, and spherical aberration were measured with Pentacam 3D anterior segment analysis system preoperatively and one month postoperatively. In addition, the relationship between EOZ and corneal HOAs was analyzed and compared between different optical-zone groups after SMILE and FS-LASIK. Results: For the same programmed optical zone, the SMILE group achieved a significantly greater EOZ than the FS-LASIK group who was measured 1-month postoperatively did (P<0.05). Meanwhile, corneal HOAs, spherical aberration, and coma in the SMILE group are significantly lower than those in the FS-LASIK group (P<0.05). For the same procedure (SMILE or FS-LASIK), the 6.0 mm group demonstrated significantly higher corneal total HOAs, spherical aberration, and coma than the 6.5 mm group did 1-month after the surgery (P<0.05). Conclusion: In both the SMILE and the FS-LASIK groups, 1-month postoperative EOZ was smaller than the programmed optical zone. EOZ in the SMILE group was larger than that in the FS-LASIK group. The larger the 1-month postoperative EOZ was, the lower corneal HOAs were. For the same programmed optical zone, 1-month postoperative corneal HOAs in the SMILE group is lower than that in the FS-LASIK group.