BACKGROUND: We observed the effect of different modified percentage of tissue alteration (mPTA) on corneal higher-order aberrations in small incision lenticule extraction (SMILE), and explored safe threshold values of mPTA for SMILE surgery. METHODS: 148 patients (270 eyes) was retrospectively analyzed and grouped into two groups based on mPTA between 24%. Mixed linear model analysis was used for preoperative and postoperative 1 week (W1), 1 month (M1), 3 months (M3), and 6 months (M6) follow-ups to compare the differences and changes in visual acuity, and corneal higher order aberrations between groups. RESULTS: Both groups showed satisfactory surgical results in the postoperative follow-up, with no statistically significant difference between the groups (F = 0.06, P = 0.81), but four of the eyes in the high mPTA group showed small refractive regression in the early postoperative period. Corn-tHOA showed a noteworthy group × time interaction effect (F = 9.308, P = 0.003), and groups had different rates of change at the time of M1, M3, M6. Similarly, Corn-tCOMA intergroup comparison was statistically different (F = 3.993, P = 0.047) and the group × time interaction effect was significant (F = 7.691, P = 0.000), with a different rate at times M1, M3. And corn-tSA varied between-group comparison (F = 11.171, P = 0.001), but the group × time interaction effect was not (F = 0.615, P = 0.606). CONCLUSION: Corneal higher-order aberrations increase after SMILE and gradually stabilized at 3 months postoperatively, which was dominated by the increase in coma and spherical aberrations, more and faster the higher-order aberrations were introduced in higher mPTA, which was mainly reflected in the variable rate of increase in corneal coma aberrations.