Scylla paramamosain is a kind of large euryhaline marine crab. As an important physicochemical parameter of seawater, salinity has a great impact on the survival, growth and quality of Scylla paramamosain. This research tested the content of non-volatile flavor substance, lactic acid and taurine on the 0, 1st, 3rd, 7th and 15th day in three salinity gradients (3, 13, 23) with HPLC (High-performance Liquid Chromatography) technology. Results have shown that in low salinity stress, the cumulative amount of free amino acids in muscle of Scylla paramamosain is more than that in hepatopancreas, while the cumulative amount of essential amino acids in hepatopancreas is more than that in muscle. In muscle, contents of three flavor amino acids are ranked as follows: sweet, bitter and delicious amino acid, and in hepatopancreas, it is bitter, sweet and delicious amino acid. The fluctuation rule of free amino acid, essential amino acid and lactic acid in Scylla paramamosain in the low salinity group is similar to that of other salinity control group, while the content of sweet amino acid, bitter amino acid, nucleotide, EUC, taurine is different from that of other salinity control groups.