Landmark-based morphometric analysis was conducted to identify variations in Chinese mitten crab Eriocheir sinensis from different well-known geographical origins around the same Changjiang River system, e.g., the Taihu Lake, Hongze Lake, Gaoyou Lake, Changdang Lake, Yangcheng Lake, Bacheng Aquaculture Water, Xinghua “Honggao” aquaculture area, and Chongming waters. Landmark coordinate values were extracted by image processing after digitalization of the carapace and the breastplate features, thereafter, processed with relative warp principal component methods, discrimination analysis, thin plate spline analysis and grid distortion. Many of the Type II landmarks were extracted by relative warp principal component analysis and they had important contributions (82.637%-97.698%) in explaining the most important variation. The discrimination analysis indicated that the carapace of male and female had exactitude distinguishing ratios of 100% while the breastplate had exactitude distinguishing ratios of 98.75% and 83.75%, respectively. All of these indicated that it was an effective method of habitat recognition of Chinese mitten crab by using landmark-based morphometric analysis, which provides some important reference and scientific basis for developing a more objective method for geographical origin identification of E. sinensis.