Accuracy of planned corneal stromal thickness (CST) reduction is essential to the safety of laser vision correction. This study was to compare the accuracy of the planned central CST reduction in small incision lenticule extraction (SMILE) and femtosecond laser-assisted in situ keratomileusis (FS-LASIK). A total of 77 patients (43 for SMILE, 34 for FS-LASIK using Custom-Q algorithm) were included in this retrospective study. At postoperative 6–18 months, the central CST reduction was overestimated by 18.49 ± 6.42 μm in the SMILE group (P < 0.001) and underestimated by 2.56 ± 7.79 μm in the FS-LASIK group (P = 0.064). The planned-achieved difference (PAD) of central CST reduction was positively correlated with preoperative manifest refraction spherical equivalent (MRSE) and with planned central CST reduction in both groups. When calculated by manifest refraction (MR) without nomogram adjustment, the central CST reduction was overestimated by 11.14 ± 6.53 μm in the SMILE group and underestimated by 2.83 ± 7.39 μm in the FS-LASIK group. The PAD of central CST reduction without nomogram was significantly narrowed in SMILE and maintained in FS-LASIK, suggesting estimation using MR without nomogram adjustment may be feasible for SMILE and FS-LASIK in clinical practice.