Inner nuclear layer(INL) microcysts at central macula are a common finding in patients with epiretinal membrane (ERM) after vitrectomy and membrane peeling. Using en face mode of optical coherence tomography (OCT) angiography, patients with ERM after surgery were retrospectively reviewed to understand the configuration and distribution of microcysts as well as their impact on visual acuity. Forty-six eligible patients were enrolled and their baseline best-corrected visual acuities improved from 20/67 to 20/29 (P < 0.01) after surgery. Twenty-eight (60.9%) patients had microcysts that appeared at a median of 5 months after the surgery and persisted for mean 16 months follow-up. The microcyst appeared as spheroidal shape with length ranged from 20 to 80 μm and widths of 80 μm in average. They tend to group in cluster with a density of 245 microcysts per mm2. The frequency of microcyst distribution was 86%, 54%, 32%, 25% and 18% at the nasal, superior, inferior, temporal quadrants and central 1 mm, respectively. Linear regression analysis showed that INL microcysts at central and temporal quadrants were associated with poorer visual acuity (P = 0.02 and P = 0.01, respectively). The presence of INL microcysts in center subfield and involved wider area is a poor prognostic factor for visual outcomes.