Triphenyltin (TPT), a kind of persistent pollutant, is prevalent in the aquatic environment and could pose a threat to coral reef fish. However, little is known about the toxicity of TPT on coral reef fish, especially regarding the representative characteristics of body coloration. Therefore, this study chose the clownfish (Amphiprion ocellaris) in order to investigate the effects of TPT exposure on its carotenoid-based body coloration under the environmentally relevant concentrations (0, 1, 10 and 100 ng/L). After TPT exposure for 60 d, the carotenoid contents were decreased and histological damage in the liver was found, shown as nuclear pyknosis and shift, lipid deposition and fibrotic tissue hyperplasia. Liver transcriptomic analysis showed that TPT exposure interfered with oxidative phosphorylation and fatty acid metabolism pathways, which related to carotenoids uptake and metabolism. Furthermore, TPT exposure led to oxidative damage in the liver, which is responsible for the changes in the antioxidant capacity of enzymes, including GSH, MDA, POD, CAT and T-SOD. TPT exposure also affected the genes (Scarb1, CD36, Stard3 and Stard5) related to carotenoid absorption and transport, as well as the genes (GstP1 and Bco2) related to carotenoid deposition and decomposition. Taken together, our results demonstrate that TPT influenced carotenoid-based coloration in coral reef fish by disrupting carotenoid metabolism, which complements the ecotoxicological effects and toxic mechanisms of TPT and provides data for the body color biology of coral reef fishes.