Purpose. To evaluate decentration following femtosecond laser small incision lenticule extraction (SMILE) and sub-Bowman keratomileusis (SBK) and its impact on higher-order aberrations (HOAs). Methods. Prospective, nonrandom, and comparison study. There were 96 eyes of 52 patients who received SMILE and 96 eyes of 49 patients who received SBK in this study. Decentration was calculated 6 months after surgery with Pentacam. HOAs and visual acuity after the surgery were examined for patients in both groups before and 6 months after surgery. Results. The mean decentration displacement in SMILE group was significantly less than SBK group (P = 0.020). 89 eyes were decentered within 0.50 mm after SMILE and SBK. The association between vertical decentration and the induced spherical aberration was insignificant in SMILE group (P = 0.035). There was an association between decentration and safety index, efficacy index, vertical coma, spherical aberration, and HOAs in root mean square (RMS, μm) after SBK (all P < 0.05). No difference was found in uncorrected and corrected distance visual acuity, safety index, efficacy index, and wavefront aberrations between the two subgroups at any delimited value after SMILE (all P > 0.05). Decentration exceeding 0.37 mm affected vertical coma and RMSh of SBK eyes (P = 0.002, 0.005). Conclusion. SMILE surgery achieved more accurate centration than SBK surgery. Vertical decentration is associated with the induced spherical aberration in SMILE.