This study applied headspace solid phase microextraction combined with comprehensive two-dimensional gas chromatography-time of flight mass spectrometry to analyze the volatile flavor compounds in the skin and scales of cultured in small cages (X), submersible cages (S), and purse seines (W). A total of 118 volatile components were detected in skin and scales of fish from X, S, and W. In addition, aldehydes, alcohols, ketones, and hydrocarbons were the dominant compounds. Significant differences were observed between the volatile components in the skin and scales of X, S, and W (<0.05). In particular, carbonyl compound and alcohol contents were highest in scales of W fish, followed by scales of those in S, and lowest in scales of fish from X. The carbonyl compound and alcohol contents in skin of fish in W were significantly higher than those in skin of fish from X and S, but no differences were detected between skin from fish in X and S. Differences in carbonyl compound and alcohol contents were directly related with polyunsaturated fatty acid (PUFA) content in the bodies of cultured using different methods. PUFA content accumulated gradually in the body of as physical activity and natural food intake increased. Therefore, the carbonyl compounds and alcohols produced by PUFAs increased accordingly. Among the volatile compounds in scales of fish held in all three enclosures, 5, 15, and 13 kinds of compounds (ROVA≥1) were selected as key odorants with relative odor activity value. The number of key odor compounds (ROVA≥1) in scales of fish from W and S were more than that in scales of fish from X. In addition, more key odor compounds were detected in scales of fish from W and S than from the other. Nine, 10, and 16 key odor compounds (ROVA≥1) were selected in skin from fish in the X, S, and W. More key odor compounds (ROVA≥1) were detected in scales from fish in W than those in skin from fish in X and S. Similarly, more key odor compounds were detected in scales of fish from W than the others. We concluded that carbonyl compound and alcohol contents in W was higher than those in X and S. In addition, the flavor composition in W was optimal. The number and variety of key odor compounds were greater in W than those in X and S, and, flavor in W was richer than that in X and S.