The morphology is an important criterion for the evaluation of carb breed quality of Eriocheir sinensis. High-quality carb breed were thought to possess patent rostral spine and verruca as well as relatively longer periopods, but it remains unclear whether these morphological characteristics can be stably inherited and be served as indicators for selective breeding of E. sinensis. Therefore, thirty-six morphological indices were used to evaluate the changes and difference of juvenile E. sinensis from pond-reared(PR) and wild-caught(WC) populations before and their offspring from the first generation (G1) and the second generation (G2) after the selective breeding programs; and the analysis methods included One-Way Analysis of variance, discriminant analysis, principal component analysis and cluster analysis for discrimination. The results showed that:(1) in One-Way Analysis of variance, there were significant differences between unselected PR and WC populations (G0) in the 16 and 15 out of 36 morphological indices for females and males respectively, and these differences disappeared gradually during selection so that no significant difference could be found in 36 morphological indices after selection for two generations (G2); (2) in discriminant analysis, the accuracy rate of discrimination were 93%-100% between unselected populations and this value decreased obviously after first and second generation of selection (G1 and G2), only 56.67%-76.67%; (3) in principal component analysis, only G0 individuals of PR and WC population could be divided into two independent groups by the first two principal components; in terms of WC populations, G0 individuals were separated from G1 and G2 individuals, and it is hard to distinguish G0, G1 and G2 individuals of PR population between each other either; (4) in cluster analysis, G0, G1 and G2 individuals of PR population clustered with G1 and G2 individuals of WC population while G0 of WC individuals clustered independently, whether females or males. In conclusion, although there was significant difference in many morphological indices between WC and PR juveniles, these differences disappeared gradually during the selection process, and the similar morphological indices were found in the juveniles of G2 between PR and WC populations. Therefore, morphological characteristics could not be used as effective indices for the selective breeding of E. sinensis.