Cyanidin-3-glucoside (C3G) is the most common anthocyanin in dark grains and berries and is a food functional factor to improve visual health. However, the mechanisms of C3G on blue light-induced retinal pigment epithelial (RPE) cell photooxidative damage needs further exploration. We investigated the effects of C3G on blue light-irradiated A2E-containing RPE cells and explored whether sphingolipid, mitogen-activated protein kinase (MAPK), and mitochondria-mediated pathways are involved in this mechanism. Blue light irradiation led to mitochondria and lysosome damage in RPE cells, whereas C3G preserved mitochondrial morphology and function and maintained the lysosomal integrity. C3G suppressed the phosphorylation of JNK and p38 MAPK and mitochondria-mediated pathways to inhibit RPE cell apoptosis. Lipidomics data showed that C3G protected RPE cells against blue light-induced lipid peroxidation and apoptosis by maintaining sphingolipids balance. C3G significantly inhibited ceramide (Cer d18:0/15:0, Cer d18:0/16:0 and Cer d18:0/18:0) accumulation and elevated galactosylceramide (GalCer d18:1/15:0 and GalCer d18:1/16:0) levels in the irradiated A2E-containing RPE cells. Furthermore, C3G attenuated cell membrane damage by increasing phosphatidylcholine and phosphatidylserine levels. C3G inhibited apoptosis and preserved the structure of mitochondria and lysosome by regulating sphingolipid signaling and suppression of MAPK activation in RPE cells. Thus, dietary supplementation of C3G prevents retinal photooxidative damage.