This study investigated the characteristics of cystoid macular edema (CME) using fundus autofluorescence (FAF) and noninvasive markers of ischemia in retinal vein occlusion (RVO) using FAF and optical coherence tomography (OCT) in 49 eyes of patients with RVO and 25 healthy eyes. Typical CME with hyperautofluorescence on FAF was demonstrated in 69.57% of patients with nonischemic RVO and 26.92% of patients with ischemic RVO (p = 0.029, p < 0.05). Disorganization of the inner retinal layers (DRIL) was observed in 13 eyes with nonischemic RVO and in 23 eyes with ischemic RVO (χ² = 6.387, p = 0.012, p < 0.05). A prominent mean limiting membrane sign (p-MLM) was present in 5 eyes with nonischemic RVO and in 15 eyes with ischemic RVO (χ² = 6.530, p = 0.011, p < 0.05). The mean optical intensity of the retinal pigment epithelium (RPE) layer, ellipsoid, and interdigital zones was 109.78 ± 19.327 in the ischemic group, significantly lower than 172.31 ± 30.527 in the nonischemic group (p = 0.001, p < 0.01). CME in ischemic RVO is less detectable on FAF than in non-ischemic RVO. DRIL, p-MLM, disruption of the integrity of the external limiting membrane (ELM), reduced optical intensity of the ellipsoid zone and RPE serve as indicators of ischemia in RVO.