In order to explore the breeding direction of morphological selection of Procambarus clarkii, the morphological characteristics of five P. clarkii basic populations from different regions in China were comprehensively analyzed by multivariate statistical analyses. The results showed that there were significant differences in most morphological parameters among populations and between sexes. In the discriminatory analysis, the most discriminant characteristics for distinguishing females among populations were body weight (BW), first abdominal segment width (FASW), third abdominal segment width (TASW) and third abdominal segment height (TASH), whereas for males, the characteristics were body weight (BW), carapace length (CL), carapace width (CW) and third abdominal segment width (TASW).The most significant variables of the differences between sexes were body weight (BW), third abdominal segment width (TASW) and double cheliped weight (DCW). This study would be beneficial to understanding the main morphological characteristics of P. clarkii, which could provide basic data of the collected germplasm resources and some reference for indicating the direction of P. clarkii morphology-based breeding. The germplasm resources with stronger abdomen, smaller carapace and smaller cheliped would be the selection targets, and all-female breeding would also be one of important breeding directions of for P. clarkii.