Cone-rod dystrophy (CORD) is one of the inherited retinal diseases that result in central visual field deterioration and decreased visual acuity (VA). In CORD patients, impaired photoreceptor cells are observed as the disruption of ellipsoid zone (EZ) on optical coherence tomography (OCT) images. In the present study, we calculated the index of residual EZ (rEZ) to quantify the function of photoreceptor cells and investigated the correlation between rEZ index and visual functions. Twenty-six eyes of 13 patients with clinical suspicion of CORD were examined. Visual field was tested with the Humphrey Visual Field Analyzer (HFA 10-2 program). We simultaneously obtained OCT images and calculated the area of decreased EZ intensity (EZa). Using the binarized OCT images, the percentage of the rEZ in a 3 × 3 mm area surrounding the macula was analyzed. To clarify interrator reproducibility, intraclass correlation coefficient (ICC) was calculated. Moreover, we investigated the association between OCT parameters and VA as well as the mean deviation (MD) value measured with HFA. The mean age of the patients was 48.5 ± 16.9 years. The mean central retinal thickness was 122.7 ± 73.2 μm. The mean EZa and rEZ were 22.2 ± 23.6 μm² and 0.35 ± 0.31, respectively. The ICC of each rEZ index was 0.91 (95% CI: 0.89 < ICC < 0.93). Multivariate analysis indicated rEZ was significantly related to logMAR VA ( p = 0.05) and rEZ and EZa were associated with the MD value ( p = 0.014 and p = 0.009, linear mixed model). Furthermore, rEZ was also associated with photopic a- and b-wave amplitudes ( p = 0.027 and p = 0.0024, respectively, linear mixed model). Taken together, the current results suggested the usefulness of rEZ quantification for predicting visual functions in CORD patients.