With the development of China's economic level and improving people's living standards, the state's supervision of food health and safety has increased. Consumer demand for many people has gradually changed from being satiated to eating well, and high-quality, environmentally friendly, and healthy aquatic products have become increasingly popular with consumers. However, intensive and high-density aquaculture causes the deterioration of water environmental conditions, the increase of anti-nutrient factors and nutritional imbalance caused by the replacement of animal protein with plant protein in feed, and changes in the growth, immunity, and digestive ability of aquatic animals caused by changes in feed nutrients, traditional processing methods, and transportation stress. The above situations encountered in aquaculture have a common impact on aquatic animals and inevitably cause a reduction in the muscle quality of aquatic animals. Therefore, improving the muscle quality of aquatic animals and the quality of aquatic products is an urgent problem with significant research value and potential. To improve aquatic quality, first, it is necessary to first identify the indicators of muscle quality in aquatic animals to improve aquatic quality. However, there is still a lack of a systematic muscle quality evaluation index system in the current aquaculture research. Therefore, this study reviewed the evaluation indices of muscle quality, including meat content, muscle nutrient composition, muscle fiber structure, muscle texture characteristics, and muscle physicochemical indices, to provide a reference for establishing scientific muscle quality evaluation indices. In addition, factors affecting muscle quality must be considered in studies aimed at improving the muscle quality of aquatic animals. Only by understanding the factors affecting muscle quality in aquatic animals can the key factors regulating muscle quality and their mechanisms be studied more comprehensively and scientifically. This study reviewed the factors affecting the muscle quality of aquatic animals, including feed nutrients, feed additives, and the culturing environment, and found that nutrients are key factors in improving the muscle quality of aquatic animals. Protein is an important nutrient, the main component of muscle, and an important indicator of muscle quality. Amino acids are the basic units of proteins and have a vital impact on muscle quality and flavor. Therefore, it is important to study the effects and mechanisms of action of amino acids on muscle quality in aquatic animals. Therefore, the effects of dietary amino acids on the muscle quality of aquatic animals were reviewed in this study, including the effects of amino acids on muscle nutrients, flavor, texture indices, and physical and chemical properties of aquatic animals. Furthermore, the effects of amino acids on muscle quality, including the promotion of protein synthesis, regulation of fat deposition, enhancement of antioxidant activity, and maintenance of intestinal health, were reviewed. In summary, this study summarized the influence of amino acids on the muscle quality of aquatic animals and its mechanism from the aspects of muscle quality evaluation indices, factors affecting meat quality, and the influence of amino acids on muscle quality, providing a reference for further research on the regulation of muscle quality by amino acids and the improvement of feed nutrients on the meat quality of aquatic animals.