Climate change and increasing instability in coastal marine environments have intensified stressors such as elevated temperature, hypoxia, salinity variation, and pollutant exposure, posing major challenges to the survival, health, and culture performance of bivalves. As economically important aquaculture species and key components of coastal ecosystems, bivalves are highly sensitive to environmental fluctuations, making their metabolic responses highly relevant to both physiological adaptation and aquaculture sustainability. Increasing evidence indicates that metabolic remodeling is an important adaptive strategy supporting bivalve tolerance to environmental stress, with amino acid metabolic remodeling emerging as one of its most sensitive and functionally important components. This review summarizes the major response patterns, key pathways, and potential regulatory mechanisms of amino acid metabolism in bivalves under different stress conditions. Different environmental stressors induce distinct yet integrated shifts in amino acid metabolism, including enhanced catabolism, carbon–nitrogen redistribution, osmotic regulation, and antioxidant defense, thereby supporting energy homeostasis and physiological stress tolerance in bivalves. By highlighting amino acid metabolic remodeling as a central mechanism of bivalve adaptation to environmental stress, this review provides insights into adaptive responses, metabolite-based indicators for monitoring aquaculture environments and bivalve health, and management strategies for improving resilience in bivalve aquaculture.