Background This study aimed to observe corneal and retinal thicknesses at 5 years after femtosecond laser-assisted in situ keratomileusis (FS-LASIK) and small incision lenticule extraction (SMILE) for myopia, investigate the effect of epithelial remodeling on refractive status and visual quality, and compare retinal thicknesses among fundus tessellation grades. Methods Patients who received FS-LASIK or SMILE 5 years before were enrolled in this cross-sectional study. After 1:1 propensity score matching, each surgical group obtained 177 patients (177 eyes). Examinations including visual acuity, refraction, corneal and retinal thicknesses, corneal higher-order aberrations (HOAs), and fundus photography were performed in this visit at 5 years after surgery. The Quality of Vision (QoV) questionnaire was used to assess visual symptoms and overall satisfaction. Corneal and retinal thicknesses between groups were compared, contributing factors were analyzed, and correlations with postoperative refractive status, HOAs, QoV scores and overall satisfaction were evaluated. Results The discrepancy of epithelial thickness between central and pericentral zones in FS-LASIK group was larger than that in SMILE group, which was negatively correlated with postoperative spherical equivalent (SE), positively correlated with spherical aberration (all P < 0.05), but not correlated with QoV scores and overall satisfaction (all P > 0.05) in both surgical groups. There was no statistical difference in stromal thickness and total corneal thickness (all P > 0.05). Most annuluses of epithelial and stromal thicknesse were linearly related to preoperative SE (all P < 0.05). The macular thickness, ganglion cell complex thickness, and retinal nerve fiber layer thickness exhibited comparable values between two surgical groups and four fundus tessellation grades, with no significant association observed with postoperative SE (all P > 0.05). Conclusion The tendency that epithelial thickness in central zone was thicker than peripheral zone was more obvious at 5 years after FS-LASIK compared to SMILE. This uneven distribution of epithelial thickness might play a role in myopic regression and the changes in HOAs, especially in patients with high myopia, but it had little effect on patients' subjective visual quality and satisfaction. Retinal thicknesses were not affected by these two surgical methods, and they did not appear to be the clinical indicators for myopic regression or fundus tessellation progression.