The majority of pond-reared Chinese mitten crab (Eriocheir sinensis) grow and fatten in freshwater. Previous studies illustrated that E. sinensis cultured in saline-alkaline water in outdoor environments showed a higher quality than that cultured in freshwater. However, it is still unclear whether salinity or alkalinity has an important positive effect on the quality of E. sinensis. This study aimed to investigate the gonadal development, edible yield, coloration, and nutritional and flavor quality of E. sinensis fattening in saline and alkaline water indoors. Results showed that there were no significant changes observed in gonadosomatic index (GSI) and other edible parameters among freshwater (FW), saline water (SW), and alkaline water (AW) during the 55-day fattening period (p > 0.05). Significantly higher a* and b* values of freeze-dried female carapace were observed fattening in SW and AW compared with that of FW (p < 0.05). The crude protein in gonad and male muscle, moisture in female muscle, and crude lipid in male muscle increased significantly from FW to SW and AW (p < 0.05). Better nutritional and flavor values were also detected in male hepatopancreas and muscles. In conclusion, numerous advantages of fattening in SW and AW were observed, including the improvement of carotenoid accumulation in freeze-dried carapace, DHA, EPA, total essential free amino acids (∑EFAA), total free amino acids (∑FAA), and total umami values (∑TUV) contents in male hepatopancreas and muscle.