The Chinese mitten crab, , is one of the most important aquaculture species in China, with a commercial yield of 729 900 tons in 2013. The main culture areas are located in three main drainage basins, i.e., the Liaohe River, the Huanghe River, and the Yangtze River. The Yangtze delta is the largest culture area among the three drainage basins. Although pond-reared populations of originated from their native habitats, i.e., the Liaohe River, Yellow River and Yangtze River, the Yangtze River population generally has the largest body size of adult crabs, the best growth performance, and superior taste among the three populations. To date, however, it is unclear whether there are any differences in gonadal development and nutritional composition of adult male among the three populations when they are cultured under similar pond conditions. In this study, we analyzed the gonadosomatic index (GSI), hepatosomatic index (HSI), meat yield (MY), total edible yield (TEY), and relative fatness (RF) of pond-cultured male , comparing the Yangtze River, Yellow River, and Liaohe River populations. Then, the proximate composition, fatty acids and amino acids composition, and essential amino acid score were compared among the three edible parts (gonad, hepatopancreas, and muscle). The results showed that the GSI was slightly higher in the Yellow River population than in the other populations, while the Yangtze River population had higher HSI, MY, TEY, and RF than those of the other two populations. However, there were no significant differences in these indicators among the three populations. The protein content in the gonad was significantly higher in the Liaohe River population than in the other two populations (<0.05), but moisture, lipid, and ash contents did not differ significantly among the three populations. The hepatopancreas of the Yangtze population had the lowest moisture content, but had higher protein, lipid, and ash contents than those of the other two populations. Compared with the Liaohe River population, the Yellow River population had significantly lower lipid content in the muscle (<0.05). The ash content in the muscle was significantly higher in the Yellow River population than in the other two populations (<0.05). The moisture and protein contents in muscle did not differ significantly among the three populations. The polyunsaturated fatty acids (PUFA) levels in the gonad were similar among the three populations, and the Yangtze population had the highest percentage of ΣPUFA, Σn6PUFA, and total highly unsaturated fatty acid (HUFA) among the three populations. For the hepatopancreas, the percentages of all PUFAs, ΣPUFA, and ΣHUFA were similar among the three populations. Compared with the Liaohe River population, the Yellow River population had significantly higher levels of C18:3n3 (LNA) and C20:5n3 (EPA) in the muscle (<0.05). The Liaohe River population had significantly higher methionine and cysteine contents in the gonad, compared with the other two populations (<0.05), and the highest contents of total essential amino acids (ΣEAA), total nonessential amino acids (ΣNEAA), and total amino acids (TAA) in the gonad. Among the three populations, the Yangtze population had the highest ΣEAA, ΣNEAA, and TAA contents in the muscle. Lysine, valine, and tryptophan were the limited amino acids in the gonad of the Liaohe River population. This population had the lowest mean essential amino acid score (EAAS) for the gonad among the three populations. In all three populations, the muscle of male crabs contained balanced amino acids and no amino acids were limiting. Together, these results suggest that there are differences in gonadal development and nutritional composition among the three populations, and that these differences may be related to different developmental stages and genetic factors.