Objective. To compare the corneal asphericity and higher-order aberrations (HOAs) of femtosecond laser-assisted in situ keratomileusis (FS-LASIK) with Smart Pulse Technology (SPT) assisted transepithelial photorefractive keratectomy (Trans-PRK) for myopia and myopic astigmatism correction. Methods. This prospective study analyzed 88 eyes of 44 patients treated with FS-LASIK and 64 eyes of 32 patients treated with Trans-PRK. All eyes had low to moderate myopia with or without astigmatism (spherical equivalent (SE) <−6.00 diopters). The uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), SE, asphericity (Q value) of the anterior corneal surface, index of surface variance (ISV), corneal higher-order aberrations (HOAs), vertical coma (Z3−1), horizontal coma (Z31), and spherical aberration (Z40) over a 6 mm diameter central corneal zone diameter were evaluated preoperatively and 1, 3, and 6 months postoperatively. Results. At 6 months, the UDVA and SE were −0.14 ± 0.06 and 0.33 ± 0.33D in FS-LASIK and −0.15 ± 0.06 and 0.35 ± 0.37D in Trans-PRK. There was no difference between the two groups in the postoperative UDVA and SE (
P
>
0.05
). After FS-LASIK and Trans-PRK, the Q values in the 6, 7, 8, and 9 mm zones and ISV of the anterior corneal surface significantly increased (
P
<
0.001
). At 1, 3, and 6 months after surgery, corneal HOA, Z3-1, Z31, and Z40 in both groups were significantly increased compared with those before surgery, with statistically significant differences (
P
<
0.001
). At 1, 3, and 6 months after surgery, the Z3−1 of the Trans-PRK group was significantly lower than that of the FS-LASIK group (
P
<
0.001
). ΔHOA and ΔZ40 were dramatically correlated with the ΔQ value for both FS-LASIK and Trans-PRK procedures. The ΔQ was significantly correlated with the preoperative SE, AD, and AD/CCT after both two procedures (all
P
<
0.001
). Conclusions. Both FS-LASIK and Trans-PRK caused the anterior corneal surface to become flatter, and the morphology of the corneal surface was irregular. Corneal HOAs were significantly increased after the two procedures. Trans-PRK using SPT introduced less corneal vertical coma than FS-LASIK. Corneal asphericity changes contributed to the corneal aberrations changes following FS-LASIK and Trans-PRK.