The Scomber japonicus (chub mackerel), belonging to the family Scombridae of the order Scombriformes, is one of the most important marine fishery catch targets in China. It is highly favored by consumers for its remarkable nutritional value. However, in recent years, S. japonicus resources have been experiencing a downward trend due to increasing fishing pressure. To compensate for the supply shortage caused by this resource decline, many countries including China have launched artificial culture programs of S. japonicus. To systematically evaluate the differences in muscle nutritional characteristics between wild and cultured S. japonicus in the coastal waters of China, and to investigate the change patterns in the nutritional composition of S. japonicus muscle under aquaculture conditions, this study collected multiple wild S. japonicus populations from the Yellow Sea, East China Sea, and South China Sea, as well as samples of two different sizes of cultured S. japonicus. The nutritional components, including moisture, crude protein, crude fat, ash, amino acids, and fatty acids, in their muscles were compared and analyzed. The results showed that the total amount of protein and fat in the muscles of both wild and cultured S. japonicus was relatively high among common marine fish species, and both possess high nutritional value. The analysis of muscle proteins and amino acids (both hydrolyzed and free amino acids) indicated that as the body size of cultured S. japonicus increases, the protein content and flavor quality of the muscles tended to decrease. However, both wild and cultured S. japonicus had a rich composition and content of essential amino acids, meeting the ideal protein standards recommended by the Food and Agriculture Organization of the United Nations/World Health Organization (FAO/WHO). Additionally, the cultured S. japonicus had a lower risk of histamine poisoning compared to the wild S. japonicus. Based on the analysis of muscle fat content and fatty acid composition, it can be inferred that the culturing process significantly increased fat accumulation in the muscle of S. japonicus. Compared to wild S. japonicus, the cultured S. japonicus had a much higher content of polyunsaturated fatty acids (PUFA), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), per unit mass of muscle, showing a more optimal fatty acid composition. In conclusion, there are differences in the nutritional characteristics of the muscles between wild and cultured S. japonicus. The culturing process can generally enhance the nutritional value of S. japonicus, reduce its food safety risks, and achieve a higher nutritional quality. The above results suggested that S. japonicus is a promising candidate for marine aquaculture and has a broad development prospect.