To figure out the different nutritional quality of S.scherzeri muscle from different habitats, this study determined and compared the nutritional compositions, as well as fatty acids composition and content of S.scherzeri. The results showed that there was significantly higher crude fat content in the muscle of S.scherzeri in upstream area than that in the muscle of S.scherzeri in downstream area (P<0.05), without significance in content of moisture, crude protein and ash between these two groups (P>0.05). There are 16 kinds of fatty acids in the muscle of S.scherzeri in upstream area and 17 in downstream area. The saturated fatty acids, monounsaturated fatty acids and polyunsaturated fatty acids occupied 35.886%, 34.184% and 29.922% in the muscle of S.scherzeri in upstream area, occupied 34.913%, 34.895% and 30.181% in the muscle of S.scherzeri in downstream area, respectively. And for the composition of fatty acid, the essential fatty acid occupied 11.735%, the ratio of ω-6/ω-3 was 0.919,EPA and DHA was 11.672% in the muscle of S.scherzeri in upstream area. The essential fatty acid occupied 9.571%, the ratio of ω-6/ω-3 was 0.781,EPA and DHA was 12.939% in the muscle of S.scherzeri in downstream area. In conclusion,the nutritive value of fatty acid in the muscle of S.scherzeri in upstream area was better than that of S.scherzeri in downstream area.