The study was conducted to compare hepatosomatic index (HSI), gonadosomatic index (GSI) in wild adult Chinese mitten crab (Eriocheir sinensis) during their catadromous migration, which were sampled from freshwater region near Zhenjiang city (defined as freshwater group) and brackish water area near Chongming Island in the estuary of Yangtze River(defined as brackish water group). After the dissection and biochemical analysis, total lipids and fatty acid composition in the hepatopancreas and muscle were further compared between the two groups. The results showed that: (1) The HSI of the males and the GSI of the females in the freshwater group were significantly higher than those of the corresponding brackish water group (P< 0.05); despite of males or females, the freshwater group had the significantly higher total lipids in the hepatopancreas than the brackish water group (P< 0.05), and there was no significant difference in total lipids in the muscle between the two groups (P> 0.05); (2) As for the hepatopancreatic fatty acid compositions, both male and female crabs from the freshwater group had the significantly higher levels of C20:1n9, C18:2n6 and C18:3n3, but the lower percentages of C18:1n7, C20:5n3 and C22:5n3 in the hepatopancreas than the brackish water group,which resulted in the fact that the freshwater group had the significantly lower levels of total n-3 polyunsaturated fatty acids (∑n-3 PUFA) and the ratio of ∑n-3 PUFA/ total n-6 polyunsaturated fatty acids (∑n-6 PUFA), but the higher ∑n-6 PUFA levels in the hepatopancreas than the brackish water group (P< 0.05); (3) As for the fatty acid compositions in the muscle, the males from freshwater group had significantly higher levels of C17:0, C18:0, C20:1n9, C18:2n6, C18:3n3 and C20:2n6, but lower percentages of C16:1n7, C20:5n3 and C22:5n3 than that of the brackish water group; thus the males from brackish water group had higher percentages of ∑n-3 PUFA and the ratio of ∑n-3 PUFA/ ∑n-6 PUFA than males from freshwater group (P< 0.05);The changing patterns of female fatty acid profiles in the two groups were consistent with those in the males, but the levels of C17:1n7 and C20:4n6 in female muscle of the freshwater group were significantly higher than those of brackish water group (P<0.05). In conclusion, when the wild adult E. sinensis migrated from freshwater area to the brackish water area in the estuary of Yangtze River, the significant decreases were found in HSI and total lipids in the hepatopancreas, but the crabs sampled from brackish water generally had the higher percentage of the total n-3-long chain PUFA (∑n-3-LC-PUFA,≥C20:2n) in the hepatopancreas and muscles than the freshwater group.