Marine fish exhibit elevated levels of arsenobetaine (AsB), while the impact and underlying mechanism of salinity on AsB biosynthesis remain inadequately explored. In this study, marine medaka (Oryzias melastigma), typically inhabiting 30‰ high salinity, were gradually acclimated to low salinities of 20, 10, and 0‰. Following acclimation, the fish were exposed to arsenate (As(V)) in their diet for 30 days. Results showed a significant accumulation of total arsenic (As) and AsB concentrations in the muscle and head tissues of the exposed fish, with these accumulations exhibiting a positive correlation with water salinity. Transcriptome analyses revealed that exposure to As(V) at low salinity may disrupt membrane components and induce cytoskeletal injuries, while at high salinity, it triggered oxidoreductase activity and transmembrane transport. Metabolome analyses indicated that low salinity induced osmotic stress, resulting in an increased requirement for amino acids to upload intracellular osmotic equilibrium in O. melastigma. Furthermore, the key organic osmolytes and amino acids, including taurine, l-methionine, guanidinoethyl sulfonate, and N-acetyl-l-aspartic acid, exhibited a negative correlation with the AsB concentration. These findings indicated that salinity can regulate osmotic balance by influencing amino acid synthesis under low salinity and stimulating AsB synthesis under high salinity conditions in O. melastigma. This study provides insights into the impact of high salinity on AsB biosynthesis, the underlying regulatory mechanisms, and implications for managing As(V) risk.