This study aims to compare the changes in the corneal wavefront aberrations and the objective visual quality resulting from two types of eye surgery-small incision lenticule extraction (SMILE) and femtosecond laser-assisted in situ keratomileusis (FS-LASIK)-in patients with moderate-to-high myopia. A prospective analysis was performed on 98 eyes of 51 patients who underwent SMILE. Additionally, 88 eyes of 45 patients who underwent FS-LASIK were analyzed. All patients underwent ocular examination preoperatively and at 1 day, 1 week, 1 month, and 3 months postoperatively. Corneal aberrations and objective visual quality were measured using the Optical Quality Analysis System II (OQAS II) and Optical Path Difference Scan III (OPD-Scan III). At postoperative 1 day and 1 week, there was a statistically significant difference in uncorrected distance visual acuity (UDVA) between SMILE and FS-LASIK (P < 0.05). Postoperative spherical (S), cylinder (C) and spherical equivalent refraction (SE) were similar between the two groups (P > 0.05). In both groups, the absolute magnitude of total higher-aberrations (tHOA), piston, vertical tilt, vertical coma, and spherical aberration (SA) increased after surgery compared to preoperative values (P < 0.05). There was no significant difference in Δhorizontal tHOA, Δhorizontal tilt, Δhorizontal coma, and Δhorizontal trefoil between the two groups (P > 0.05), and the FS-LASIK had higher Δvertical trefoil and ΔSA (P < 0.05) but lower Δpiston, Δvertical tilt, and Δvertical coma than the SMILE group (P < 0.05). There was a rise in objective scattering index (OSI) and a decline in both modulation transfer function (MTF) cutoff and Strehl ratio (SR) after surgery compared to preoperative values in both groups (P < 0.05). There was a statistically significant difference in the OSI at 1 day and 3 months between the two groups (P < 0.05). Postoperative MTF cutoff and SR were similar between the two groups (P > 0.05). Postoperative OSI was positively correlated with corneal tHOA (0.261 ≤ R ≤ 0.483, P < 0.05) and was negatively correlated with vertical tilt and vertical coma (-0.315 ≤ R ≤ -0.209, P < 0.05) in both groups. While both SMILE and FS-LASIK can effectively correct moderate-to-high myopia, there is an increase in corneal aberrations and a postoperative delay in objective visual quality. The cornea may require a longer recovery period in the SMILE. OPD-Scan III combined with OQAS II is a useful supplementary inspection for assessing the optical quality following refractive surgery.