Samples from two regions (Zhanjiang and Haikou) and two size groups (300~400 and 500~600 g/fish) were selected to investigate the effects of aquaculture region and size specification on the quality characteristics of Trachinotus ovatus. Quality indicators, including morphology, body color, nutritional composition, and flavor, were analyzed. The results showed that the b* values of the body (excluding the abdomen), total umami amino acids (large-size: 26.69 mg/100 g; small-size: 25.72 mg/100 g), and inosine monophosphate content (large-size: 247.85 mg/100 g; small-size: 235.16 mg/100 g) of T. ovatus from the Zhanjiang region were significantly higher than those from Haikou. Muscles from large-size samples had a lower water content (Zhanjiang: 68.48%; Haikou: 71.69%), but higher fat (Zhanjiang: 9.96%; Haikou: 7.43%) and protein contents (Zhanjiang: 19.48%; Haikou: 18.57%). Significantly higher levels of bitterness, bitter aftertaste, hypoxanthine, and inosine were detected in small-size samples (Zhanjiang: 10.13 mg/100 g; Haikou: 12.04 mg/100 g) than in large-size samples (Zhanjiang: 6.88 mg/100 g; Haikou: 8.28 mg/100 g). Analysis of volatile flavor compounds revealed higher alcohol levels in large-size samples, whereas aldehydes were more abundant in smallsize samples. In conclusion, Zhanjiang-farmed T. ovatus exhibited more vivid body color and more pronounced flavor characteristics. Higher nutritional value was observed in large-size samples, while significant differences in flavor profiles and volatile flavor compounds were detected among different size groups. This study provides theoretical guidance for future quality control and aquaculture processing.