This study investigated the flavor quality differences between the edible parts from green and white carapace strains of adult Eriocheir sinensis. The comparison of odor and taste of edible parts, including muscles, ovaries, and hepatopancreas, was conducted through sensory evaluation and quantitative analysis of flavor compounds. The results indicated that the contents of glutamic acid ((0.56 ± 0.03) mg/g vs. (0.43 ± 0.01) mg/g) (P < 0.01), 5ʹ-inosine monophosphate ((17.13 ± 1.36) mg/100 g vs. (12.37 ± 0.29) mg/100 g) (P < 0.05), and equivalent umami concentration ((4.34 ± 0.24) g monosodium glutamate (MSG)/100 g vs. (3.34 ± 0.09) g MSG/100 g) (P < 0.01) in the muscles of white carapace crabs were significantly higher than those of green carapace crabs, resulting in a stronger umami. In contrast, the ovaries showed opposite results. For the hepatopancreas, total bitter free amino acids ((4.28 ± 0.37) mg/g) and nucleotides (inosine and hypoxanthine) were significantly lower in the white carapace strains than in the green carapace strains crabs (P < 0.05). In addition, the content of characteristic aroma substances is higher in the muscles (2-octanone, 3-phenylpropanal) and ovaries (β-citronellol) of white carapace crabs, as well as in the hepatopancreas ((E,E)-2,4-nonadienal, benzoic acid ethyl ester, β-citronellol) of green carapace crabs. In summary, the white carapace crabs outperform the green carapace crabs in most flavor attributes, suggesting that the white carapace crabs have great promotional potentiality. The research results provide a theoretical basis for the evaluation of germplasm resources and further breeding of white carapace strains of E. sinensis.