Saline–alkaline aquaculture has become an important breakthrough in expanding the space available for aquaculture in China. However, the biochemical composition and quality of Eriocheir sinensis reared in carbonate alkalinity water are still unclear. Therefore, this study investigated the edible yield, coloration, and nutritional and flavor quality of Eriocheir sinensis. A significantly lower gonadosomatic index (GSI), meat yield (MY), and total edible yield (TEY) were detected in intensive pond (IP) samples than those in semi-intensive reed wetland (SIWR) (p < 0.05). Six color parameters in the hepatopancreas (p < 0.05) differed between IP and SIRW. The contents of crude protein and fat in the female hepatopancreas of IP were significantly higher than those in SIRW (p < 0.05). The concentrations of total monounsaturated fatty acids (∑MUFA), total essential fatty acids (∑EFA), and hypocholesterolaemic/hypercholesterolaemic ratio (h/H) in the female edible tissues checked were higher in IP than those in SIRW, with significant differences including ∑MUFA in the hepatopancreas and ovary, ∑EFA in the muscle, and h/H in the ovary (p < 0.05). Higher total free amino acid (∑FAA) contents of muscle were detected in SIRW than that in IP samples. Significantly higher K, Ca, Mg, Fe, and Zn contents in the ovary were detected in SIRW samples compared to IP (p < 0.05). Overall, Eriocheir sinensis reared in carbonate-alkalinity water is an important source of nutrients.