Purpose To investigate the corneal epithelial thickness topography with optical coherence tomography (OCT) and its relationship with vision quality in epithelial basement membrane dystrophy (EBMD). Methods 45 eyes of EBMD patients, 26 eyes of dry eye (DED) patients and 22 eyes of normal subjects were enrolled. All participants were subjected to 9-mm corneal epithelial mapping with OCT and vision quality was assessed with the optical quality analysis system using the objective scatter index (OSI). Central, superior, inferior, minimum, maximum, and standard deviation of epithelium thickness (Irregularity), were analysed and correlations with the OSI were calculated. Results The mean (±SD) central, inferior and maximum epithelial thicknesses of the EBMD patients (respectively, 56.4 (±8.1) μm, 58.9 (±6.4) μm, and 67.1 (±8.3) μm) were thicker compared to DED patients ( P <0.05) and normal subjects ( P <0.05). We found greater irregularity of epithelial thickness in EBMD (5.1±2.5 μm) compared to DED patients (2.6±1.0 μm) ( P = 4.4.10 −6 ) and normal subjects (2.1±0.7 μm) ( P = 7.6.10 −7 ). The mean OSI was worse in EBMD patients than in DED patients ( P = 0.01) and compared to normal subjects ( P = 0.02). The OSI correlated with the epithelial thickness irregularity (Spearman coefficient = 0.54; P = 2.65.10 −5 ). Conclusions The OCT pachymetry map demonstrated that EBMD patients had thicker corneal epithelium in the central and inferior region. These changes were correlated with objective measurements of vision quality. This OCT characterisation of the EMBD provides a better understanding of the epithelial behaviour in this dystrophy and its role in vision quality.