To compare the corneal epithelial remodeling in eyes with high astigmatism that had small incision lenticule extraction (SMILE) and femtosecond laser-assisted laser in situ keratomileusis (FS-LASIK). Seventy-four patients with myopic astigmatism of greater than -2.00 diopters (D) and little binocular difference in spherical equivalent were included in this contralateral comparative study. All patients received SMILE in one eye and FS-LASIK in the other eye randomly. The corneal epithelial remodeling pattern was mapped using the latest RTVue spectral-domain optical coherence tomographer (Optovue) by region. Satisfactory refractive correction was achieved in all enrolled eyes with either SMILE or FS-LASIK. The corneal epithelium gradually thickened following surgical cylinder correction, distributing mainly along the flat medium. The corneal epithelium proliferation is milder centrally but more pronounced in the mid-peripheral area after SMILE, compared with FS-LASIK. The flat-steep difference in corneal epithelial thickness (CET) is evident in the mid-peripheral and peripheral areas, which is more obvious in SMILE. Residual cylinder was positively correlated with CET in eyes that had FS-LASIK, but not SMILE. More importantly, these epithelial changes were positively correlated with the ablation depth and higher order aberrations following surgical refractive correction. The postoperative CET map varied between SMILE and FS-LASIK. In eyes with high astigmatism, SMILE surgery is followed by milder and more stable corneal epithelial thickening. Moreover, the corneal epithelium is sensitive to stromal ablation and corneal remodeling is crucial to the postoperative visual quality. This study rigorously distinguished the CET difference between SMILE and FS-LASIK in astigmatic eyes and shed light on subsequent research. [J Refract Surg. 2024;40(10);e728-e741.].