Cold stress can cause metabolic disorders or death in aquatic organisms through severe effects on physiological and biochemical processes. The present paper reviewed the effects, mechanism, and control of the mechanisms of cold-stress effects and control of energy, protein, fat, and nucleic-acid metabolism in aquatic animals, especially in fish, with the ultimate goal of reducing or preventing cold-stress related damage. Future studies should investigate these questions in a multidisciplinary fashion, incorporating molecular techniques to understand cold-stress effects on the molecular, cellular, and tissue levels. Multiple measures are necessary to develop sustainable, lower-risk fisheries, including the improvement of environmental conditions, genetic engineering and breeding cold-resistant species, along with increasing cold-stress resistance through dietary (supplementation of proteins, polyunsaturated fatty acids, trace elements, and other nutrients).