To investigate potential variances in fish muscle quality under different culture modes and their causes, this study focused on the bighead carp (Hypophthalmichthys nobilis) as a target object. Samples were collected and observed in the Wanghu Lake (Wanghu Lake stocking group) and the surrounding culture ponds (pond culture group) in Hubei Province. The appearance, texture, nutritional value, and flavor characteristics of the back muscles of the two groups of bighead carp were compared. Additionally, the water quality and feed biological composition of the two groups were compared. Results showed that: (1) The intraperitoneal fat (IPF) and hepatopancreas somatic indices (HSI) of bighead carp raised in the Wanghu Lake stocking group were significantly lower than those in the pond culture group (P＜0.05). However, there was no significant difference between the two groups in terms of condition factor (CF) and viscerosomatic index (VSI) (P＞0.05). The luminance value (L^* ) and whiteness value (W) of back skin and meat of bighead carp in the Wanghu Lake stocking group were significantly higher than those in the pond culture group (P＜0.05). (2) The elasticity and cohesion of the bighead carp muscles in the Wanghu Lake stocking group were higher than those in the pond culture group (P＞0.05), whereas hardness was significantly lower than that in the pond culture group (P＜0.05). (3) The water and crude protein content of bighead carps in the Wanghu Lake stocking group were significantly lower than those in the pond culture group (P＜0.05). The crude fat content was significantly higher than that in the pond culture group (P＜0.05). The essential amino acid content and score of bighead carp in the Wanghu Lake stocking group were significantly higher than those in the pond culture group (P＜0.05). The essential amino acid (EAA)/toal amino acid (TAA) values of the Wanghu Lake stocking and pond culture groups were 41.24% and 40.84%, the ratio of EAA/nonessential amino acid (NEAA) was 84.18% and 83.03%, respectively, meeting the FAO/WHO ideal model standards. However, the levels of monounsaturated and polyunsaturated fatty acids in the Wanghu Lake stocking group were significantly higher than those in the pond culture group (P＜0.05). The concentrations of Ca and Zn in the muscles of bighead carp in the Wanghu Lake stocking group were higher than those in the pond culture group (P＞0.05). (4) The proportion of fresh amino acids was higher and the proportion of bitter amino acids was lower in the Wanghu Lake stocking group. The highest odor activity values were observed for the grassy odor hexanal and fatty odor 1-octanal in the Wanghu Lake stocking and pond culture groups, respectively. Additionally, the content of volatile compounds such as 1-hexanol and 3-pentanone in the Wanghu Lake stocking group was lower than that in the pond culture group, and the relative odor activity value (ROAV) of these volatile compounds in the pond culture group was lower than that in the pond culture group. The results showed that bighead carp reared in the Wanghu Lake stocking group had better morphological characteristics, muscle nutrition, and flavor quality than those reared in the pond culture group, associated with differences between the culture environment and natural bait. The conclusions of this study provide a theoretical reference for the development of large-scale ecological fisheries.