Coral reef fish exhibit vivid carotenoid-based coloration that plays an important role in communication and camouflage within the complex reef ecosystems. However, the molecular mechanisms underlying carotenoid coloration in these fish remain elusive. In this study, we explored the color differentiation process in Plectropomus leopardus, induced by dietary carotenoid intake, using integrated histological observations and multi-tissue transcriptomic analyses. We found that individuals with red coloration (B-AX-R) displayed an increased capacity for carotenoid absorption, transport, and deposition, along with enhanced melanin removal; however, in non-reddened individuals (B-AX-B), carotenoids were primarily used for immunity and other cellular processes rather than pigmentation. Notably, scavenger receptor Class B member 2c (scarb2c) emerged as a key gene responsible for coloration by regulating pathways involved in carotenoid uptake and transport, with interactions involving Apolipoprotein A-I (APOA1), Apolipoprotein A-IV (APOA4), and Apolipoprotein E (APOE). Through integrated metabolomics, the molecular mechanism underlying carotenoid coloration was revealed, in which scarb2c mediates a regulatory network that coordinates key metabolites, including 5b-Cyprinol, KAKA, and creatine, along with other genes involved in absorption and transport. These findings provide the first comprehensive insight into carotenoid coloration in coral reef fish and contribute to our understanding of the signaling functions associated with coloration in coral reef ecosystems.