Background: To compare the anatomical and functional outcomes of the inverted internal limiting membrane (ILM) flap technique and the complete ILM removal in the treatment of large stage 4 macular hole (MH) > 400 μm and to evaluate reconstructive anatomical changes in foveal microstructure using spectral-domain optical coherence tomography. Methods: This is a retrospective, consecutive, nonrandomized comparative study of patients affected by idiopathic, myopic or traumatic stage 4 MH (minimum diameter > 400 μm) treated with 25-gauge pars-plana vitrectomy with either complete ILM peeling (n = 23, Group 1) or inverted ILM flap technique (n = 23, Group 2), between August 2016 and August 2018. Main outcomes measured were the MH closure rate assessed by spectral-domain optical coherence tomography and the best-corrected visual acuity (BCVA) at six months. Foveal microstructure reconstructive changes were evaluated using SD-OCT to determine predictive factors of postoperative BCVA. Results: Closure of MH was achieved in 16/23 cases of Group 1 (70%) and in 22/23 cases of the Group 2 (96%). Surgical failure was reported in 6 cases of Group 1 and 1 case of Group 2. The MH closure rate was significantly higher with the inverted ILM flap technique (P-value = 0.02). Average BCVA (LogMAR) changed from 1.04 ± 0.32 to 0.70 ± 0.31 in Group 1 and from 0.98 ± 0.22 to 0.45 ± 0.25 in Group 2 (P-value = 0.005) at 6 months. Improvement in BCVA (> 0.3 LogMAR units) was statistically higher in the Group 2 (P-value = 0.03). Restoration of foveal microstructure was significantly higher in the Group 2 at 6 months (52% vs 9%, P-value < 0.01). In Group 2, the integrity of the external limiting membrane at 3 months postoperatively was the only significant feature correlated with postoperative BCVA at 6 months (r = 0.562; P-Value = 0.01, forward stepwise regression analysis). Conclusion: Inverted ILM flap technique is more effective than the classic ILM peeling for the closure of large stage 4 MHs > 400 μm, improving both anatomical and functional outcomes. Early recovery of the external limiting membrane at 3 months is a positive predictive value of postoperative BCVA 6 months after inverted ILM flap technique.