Nutrient richness and fast‐growing rate have rapidly advanced the aquaculture of Hexagrammos otakii. The current farming methods of H. otakii include wild stocking, cage culture and factory culture; however, the influence of each style on this species is unclear. This study aimed to establish and compare the nutritional profiles, muscle quality and physiological status of wild (WF), factory‐cultured (FC) and cage‐cultured (CC) H. otakii. Haematological parameters revealed remarkable differences in haemoglobin, haematocrit, mean corpuscular volume and platelet levels between the wild and cultured H. otakii. The proximal composition showed significantly higher and lower levels of crude lipids and proteins, respectively, in the CC group than that in the WF group. Likewise, the WF group exhibited significantly higher scores for texture attributes, such as hardness and springiness in addition to the significantly higher calcium and selenium contents than that in the cultured groups. Moreover, significant variations were determined in liver antioxidant capacity with a higher malondialdehyde content and glutathione peroxidase activity in the CC group than that in the other groups. Furthermore, the levels of all amino acids as well as polyunsaturated fatty acids and docosahexaenoic acid were significantly higher in the cultured groups than those in the WF group. In summary, regular consumption of cultured H. otakii may provide superior health benefits than that of wild H. otakii on the basis of the nutritional structure of muscle; however, wild H. otakii has a better taste and richer mineral composition.