Benzophenone-3 (BP-3) is a UV filter that is ubiquitously present in the environment due to its photostability and degradation resistance and has wide applications in personal care products. BP-3 will eventually be discharged into the ocean. Studies shows BP-3 interferes with endocrine system of aquatic organisms, especially fish. However, the toxicity and mechanisms of subacute exposure of the coral reef fish to BP-3 remain elusive. Here, we exposed the one-month-old clown anemonefish to BP-3 at 1 and 10 μg/L for 14 and 28 days, respectively. After chronic exposure, the effects of BP-3 on the growth of clown anemonefish were investigated in terms of growth-related hormones, immune enzyme activity, digestive enzyme activity, transcriptional profiling of feeding- and obesity-related genes and digital RNA sequencing. The body weight in the BP-3 groups were abnormally increased (1 μg/L group in 14 days treatment and all groups in 28 days treatment), altered insulin content (28 days exposure), immune-related and digestive-related enzymatic activities. At the molecular level, BP-3 interferes with the expression of feeding- and obesity-related genes. Digital RNA sequencing analysis showed that BP-3 interferes with Kyoto encyclopedia of genes and genomes (KEGG) pathways related to growth, social behavior (learning behavior), Mitogen-Activated Protein Kinase (MAPK) signaling pathway, PI3K-Akt signaling pathway, and insulin secretion. Notably, in the insulin secretion, BP-3 induced Ca2+ up-regulation that may damage β cells. Growth abnormalities and social behavior (learning behavior) KEGG pathway disturbances may have potential impacts on populations of clown anemonefish. Our results reveal the toxicological effects of subacute exposure to BP-3, and provides insight into the effects and mechanisms of BP-3 on clown anemonefish growth.