This study scrutinized the nutritional quality and serum biochemical indices of grass carp () cultivated in traditional pond intercropping (TPI) and in-pond raceway system (IPRS) aquaculture setups. The findings showed that the TPI group exhibited a superior water-holding capacity, while the IPRS showcased heightened crude lipid content and levels of textural properties such as springiness. Moreover, significant differences emerged in the fatty acid profiles, with the TPI group manifesting higher total polyunsaturated fatty acids (ΣPUFAs), EPA, DHA, and Σn-3, while the IPRS group exhibited elevated total saturated fatty acids (ΣSFAs). In terms of amino acids, valine and histidine levels were notably higher in the IPRS group, whereas lysine levels were reduced. Volatile compound analysis revealed significant variations, with the IPRS group containing more volatile substances with a better aroma, resulting in a better odor. The IPRS group performed better in serum biochemistry analysis. Additionally, grass carp in the IPRS group displayed an improved structure and greater coverage area of the visceral peritoneum, appearing lighter in color compared to the TPI group. TPI mainly influences nutritional elements; IPRSs primarily affect muscle texture, serum biochemistry, and overall health. This study aims to fill the gap in quality comparison research and provide an important scientific basis.