Objective To compare the therapeutic effect of epithelial flap removed laser subepithelial keratomileusis (LASEK) and femtosecond laser assisted LASIK (FS-LASIK) in the treatment of moderate and low myopia. Methods A total of 103 patients (103 eyes) of low and moderate myopia were selected, 51 patients (51 eyes) were treated with LASEK and 52 patients (52 eyes) were treated with FS-LASIK. Data of uncorrected visual acuity (UCVA), best corrected visual acuity (BCVA), residual equivalent spherical degree (SE), total high-order aberrations (HOAs), spherical aberration, coma and trefoil were examined before operation and 1month and 3 months after operation, and compared between two groups of patients. Results There were no significant differences in UCVA and BCVA 1 month and 3 months postoperatively between the two groups. SE shifted to myopia direction in LASEK group compared with that of FS-LASIK group 1 month postoperatively (P＜0.05), but reached a similar level 3 months after surgery. The HOAs and spherical aberration were significantly increased 1 month and 3 months postoperatively compared with those before operation in LASEK and FSLASIK groups (P＜0.05). Coma was significantly increased 1 month postoperatively in FS- LASIK group and returned to the preoperative level 3 months postoperatively, while it remained at baseline 1 month and 3 months postoperatively in the LASEK group. The HOAs and coma were significantly higher 1 month postoperatively in FS-LASIK group compared to those of LASEK group (P＜0.05), while they reached a similar level 3 months postoperatively. Conclusion The therapeutic effect of epithelial flap removed LASEK can reach a level equal to FS-LASIK at the early stage after surgery. It is a good selectable choice for patients with low to moderate myopia.