This study was designed to investigate gonadosomatic index (GSI), hepatosomatic index (HSI), meat yield (MY), total edible yield (TEY) and relative fatness (RF), and then, their proximate composition, fatty acids and amino acids composition and essential amino acid score were further detected and compared for the three edible parts (gonad, hepatopancreas and muscle) of pond-cultured female Eriocheir sinensis among Yangtze, Huang and Liao River populations. The results are shown as follows:(1) There were significant differences in the speed of ovarian development and GSI among three populations; the Liao River population had the highest GSI while Yangtze population had the lowest GSI during the period of August to end of September among three populations; however, the similar GSI was found between Liao River and Huang River populations in late October. (2) When the females had the similar GSI and body weight, no significant differences were found in HSI, MY, TEY and RF among three populations. (3) Female from three populations had the similar proximate composition for each edible part, while the Yangtze population had the significantly higher ash content in hepatopancreas and muscle than the other two populations. (4) For the fatty acid compositions in the ovaries, Yangtze population had the highest percentage of C22:6n3 (DHA) among three populations; except for C20:1n9 and C20:4n6 in the hepatopancreas, three populations females had the similar fatty acid composition in hepatopancreas and muscle. (5) The ovaries of Yangtze population had the significantly higher contents of phenylalanine, tyrosine, tryptophan, aspartic acid and serine than Liao River population; for the amino acid contents in the muscle, Huang River population had the highest contents for most amino acids, leading to the significantly higher total amino acid (TAA) than that of the other two populations. (6) No restrictive amino acids were found in the ovaries or muscle of three populations; the ovaries of Yangtze population had the highest mean essential amino acid score (EAAS) while the muscle of Huang River population had the highest mean EAAS among the three populations; despite of populations, the mean EAAS of ovaries was higher than that of muscle. In conclusion, Yangtze population had the slowest speed of ovarian development among three populations, while the fastest ovarian development was found in Liao River population. Females from three populations had the similar proximate composition and fatty acids levels in the three edible parts. Although the significant differences were detected for the contents of many amino acid in the muscle among three populations, no restrictive amino acids were found in ovaries and muscle.