As an economically important aquaculture species in China, the spotted sea bass (Lateolabrax maculatus) has flourished and made significant contributions to the national fishery economy over the past few decades. However, the “south–central–north relay” pattern of cross-regional farming in L. maculatus has caused germplasm mixing among farmed populations across China, which has become a major constraint on the sustainable development of the industry. Therefore, understanding the variations in phenotype among populations in major production areas, and assessing the shaping effect of aquaculture environments, are crucial for improving the overall quality of L. maculatus. In this study, 310 market-sized L. maculatus from three representative production areas in Guangdong, Fujian, and Shandong were examined. Nineteen phenotypic indicators, encompassing both morphological and muscle texture traits, were compared using principal component and hierarchical cluster analyses, and further integrated with nutritional quality evaluation to provide a comprehensive assessment of regional differences in morphology and quality. The results showed that (1) although principal component and cluster analyses confirmed the occurrence of germplasm admixture among populations, significant morphological and muscle texture traits differences were still observed among regions. L. maculatus from Guangdong exhibited a phenotype characterized by higher fullness (1.90 ± 0.15%) and body height (9.64 ± 0.38 cm), but shorter body length (35.21 ± 1.45 cm) and caudal peduncle (7.03 ± 0.41 cm), as well as a smaller head (10.13 ± 0.57 cm) and stronger muscle adhesiveness (?25.05 ± 6.73 g*s). L. maculatus from Fujian showed a more slender body shape with a well-developed caudal peduncle, and exhibited the highest values in key texture parameters, including hardness (7069.34 ± 536.63 g) and springiness (0.69 ± 0.06). The Shandong population displayed a general body shape similar to that from Fujian, but with a more elongated caudal peduncle (9.06 ± 0.74 cm). (2) The muscle nutritional profiles of L. maculatus from the three regions exhibited distinct characteristics, each showing differentiated advantages. L. maculatus from Guangdong had higher lipid content (3.61 ± 1.51%) and a more balanced amino acid composition. The Fujian population showed higher protein (20.71 ± 0.59%) and lower lipid content (1.80 ± 0.76%), along with a higher proportion of umami amino acids (5.89 ± 0.21 g/100g), resulting in superior flavor quality. The Shandong population was characterized by markedly higher EPA and DHA contents (7.46 ± 0.65% and 23.01 ± 1.16%, respectively), demonstrating the most prominent advantage in functional fatty acid nutrition. (3) Environmental variation, especially in annual mean temperature and salinity, emerged as the major force driving morphology, muscle texture traits and nutritional divergence in L. maculatus. Pearson correlation analysis demonstrated that caudal peduncle length, EPA and DHA proportions, and crude protein were strongly negatively correlated with temperature but positively correlated with salinity, whereas fullness, ∑ω-6 PUFA, and crude lipid content showed opposite correlations. Therefore, under the current aquaculture model, stable production of L. maculatus products with specific quality advantages can still be achieved through scientific regulation of the aquaculture environment, even when germplasm sources are complex. These findings provide a scientific basis for differentiated brand development of L. maculatus across regions and offer theoretical support for environment-based quality improvement and targeted breeding under germplasm admixture, which are of great significance for enhancing product quality, efficiency, and sustainability of the L. maculatus industry.