Purpose This study compares the posterior corneal elevation and corneal biomechanics after small incision lenticule extraction (SMILE) and laser-assisted subepithelial keratomileusis (LASEK) for myopia correction in a short-and long-term observation. Methods This prospective study included 32 patients in the SMILE group and 32 patients in the LASEK group. Corneal posterior central elevation (PCE), posterior mean elevation (PME), corneal back power (Kb), and anterior chamber depth (ACD) were evaluated with Pentacam, and intraocular pressure (IOP), corneal hysteresis (CH), and corneal resistance factor (CRF) were evaluated with the ORA at pre-operation and 3 months and 3 years post-operation. Results Three months post-operatively, CH, CRF, and IOP decreased significantly and central posterior surface shifted backward in both groups (p < 0.05). CH was lower in the LASEK group (p = 0.03) and change of CH and CRF per unit corneal tissue removed (ΔCH/ablation depth (AD) and ΔCRF/AD) was lower in SMILE than in LASEK (p = 0.01, 0.03). Three years postoperatively, the PME shifted more posteriorly in LASEK (p = 0.04), but was stable in SMILE (p = 0.06). Kb flattened and ACD was shallower in both groups (compared to preoperative data, p < 0.001). CH in the LASEK group increased and is comparable to that in the SMILE group at 3 years post-operative. Conclusion Both SMILE and LASEK can change the posterior surface and corneal biomechanics. SMILE may have less influence on corneal biomechanics than LASEK at an early stage post-operative in terms of per unit corneal tissue removed, but the effect became comparable in a long-term observation.