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The mud crab (Scylla paramamosain) is an important mariculture species, which has been successfully cultivated in inland saline-alkaline water of China. However, the study on the flavor quality of mud crab cultivated in inland saline-alkaline water has not been reported. The aim of this study was to investigate and compare the non-volatile flavor substances in the hepatopancreas and muscles of mud crabs cultured in inland saline-alkaline water (IS, 1.5 psu), coastal low salinity seawater(CS, 5 psu) and normal salinity seawater(NS, 13 psu). The results showed that there were no significant differences in total free amino acids (TAA) and essential amino acids (EAA) in muscle and hepatopancreas among the three groups. The contents of glycine (Gly) and alanine (Ala) in muscle and hepatopancreas in IS group were significantly higher than those in NS and CS groups. Taurine (Tau) content in IS-♂ group was significantly higher than that in NS-♂ group. The results of the principal component analysis showed that the similarity of amino acid composition and content in muscle and hepatopancreas of each population was related to the culture environment. To sum up, the mud crabs cultured in inland low saline-alkaline water can maintain the balance of total amino acid and essential amino acid content, the sweet flavor of edible parts was slightly enhanced, while the equivalent umami concentration was decreased. ● Inland saline-alkaline culture is a new way for the development of mud crab industry. ● Inland low saline-alkaline culture has an influence on the flavor of mud crabs. ● The contents of Gly and Ala in the muscle of saline-alkaline mud crabs are higher. ● The changes of free amino acids are related to osmoregulation. [ABSTRACT FROM AUTHOR]