Identification of composition characteristics of major and trace elements in wild mitten crabs (Eriocheir sinensis) from different water systems is important for protected geographical indication as well as food quality control and safety. In this study, inductively coupled plasma-mass spectrometry was employed to measure the contents of 23 elements in the muscle samples of wild Eriocheir sinensis from three water systems (Suifenhe, Nanliujiang, and Liaohe). The results of Kruskal–Wallis one-way ANOVA test comparisons revealed that most elements were significantly different in the samples collected from three water systems (P < 0.05). Geographic origin discrimination was achieved using principal component analysis in combination with hierarchical cluster analysis (HCA) and stepwise linear discriminant analysis (S-LDA). The HCA results showed the potential of eight characteristic elements for exploratory hierarchical clustering of the samples from three water systems; however, the clustering effect was unsatisfactory. The discrimination accuracy of S-LDA model for the samples from three water systems and that in cross-validation reached 100%. The health risk assessment further revealed that the normal level consumption of wild Eriocheir sinensis did not pose an appreciable health risk to consumers.