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Chinese water chestnuts (CWCs) have high nutritional value and are important in the field of food and medicine. However, there may be significant differences between CWCs from different regions. This study focused on the differences in nutritional quality and functional active substance content of CWCs from nine different origins in China and established an evaluation method to assess these differences. It was found that the total phenolic and total flavonoid contents of CWCs peel were much higher than those of pulp, with the peel of CWCs from origin II having the highest total phenolic content and a high DPPH (2,2-Diphenyl-1-picrylhydrazyl) radical scavenging rate. The starch content of the pulp of CWCs from origin V was significantly higher than that in the other origins, and the peel from origin IX and the pulp from origin IV had the highest soluble sugar levels. Principal component analysis (PCA) revealed that the peel quality was primarily affected by the browning degree, soluble solids, and antioxidant capacity, while the pulp exhibited a stronger correlation with total flavonoids and protein. The comprehensive evaluation demonstrated that origin I, origin VII, and origin IX were relatively high-quality peel resources, while origin II, origin V, and origin VIII had better pulp quality than the other groups. This study aimed to elucidate the differences between various production areas of CWCs and provide a reference for the deep processing of CWCs. Full article