Salinity fluctuations are key environmental drivers that shape physiological homeostasis in euryhaline teleosts by altering osmotic balance and energy allocation. In this study, marine medaka (Oryzias melastigma) was used to elucidate skeletal muscle adaptation to chronic low-salinity stress by integrating histology, transmission electron microscopy (TEM), antioxidant indices, transcriptomics, and metabolomics. Offspring (F₁) derived from low-salinity-acclimated parents were reared at a salinity of 2.5‰ and sampled at 4 months, with fish from 25‰ seawater serving as controls. Low salinity significantly reduced the mean cross-sectional area of myofibers while increasing fiber density. TEM revealed a marked widening of the I-band without changes in sarcomere length, suggesting an altered actin–myosin overlap that may help maintain contractile performance under osmotic stress. Biochemical assays showed unchanged catalase activity but significantly elevated total antioxidant capacity (TAC) and malondialdehyde (MDA)levels, indicating enhanced lipid peroxidation accompanied by compensatory activation of the antioxidant defense network. Transcriptome profiling identified 1266 differentially expressed genes (985 downregulated, 281 upregulated), enriched in cytoskeletal and contractile remodeling (desmosomes, myofibrils, myosin filaments) as well as signaling pathways including Wnt/β-catenin and mTOR. Metabolomics detected 112 differential metabolites; the pro-inflammatory oxidized phospholipid POVPC accumulated, 3-hydroxycoumarin levels increased, and uric acid levels decreased. Enrichment analyses highlighted autophagy, mTOR signaling, and the sulfur relay system, suggesting a metabolic shift from hypertrophic growth towards maintenance and repair. Collectively, marine medaka adapts to chronic low salinity through multi-layered remodeling of myofiber architecture, cytoskeletal networks, and integration of antioxidant and autophagy mechanisms. These findings provide a multi-omics framework for understanding muscle plasticity under hypo-osmotic stress and offer candidate targets for optimizing brackish and freshwater aquaculture practices.