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Chrysanthemi Flos ‘Hangbaiju’ (HBJ) is a common Chinese medicinal material with the same origin as the medicinal and edible cognate plant in China, whose quality is seriously affected by the place of origin. In this study, four stable isotope ratios (δ15N, δ2H, δ13C, and δ18O) and 44 elements were detected and analyzed in 191 HBJ flower samples from six locations in China to trace the origin of HBJ. An ANOVA analysis of δ15N, δ2H, δ13C, and δ18O values, as well as milti-elements, showed that there were significant differences among the six places of origin. Partial least squares discriminant analysis (PLSDA) and one-class partial least squares discriminant analysis (OPLS-DA) models were established to trace the origin of HBJ from these six locations. The results showed that the classification effect of the PLSDA model is poor; however, the established OPLS-DA model can distinguish between products of national geographic origin (Tongxiang City, Zhejiang Province, China) and samples from other origins, among which Ni, Mo, δ13C, Cu, and Ce elements (VIP > 1) contribute the most to this classification. Therefore, this study provides a new method for tracing the origins of HBJ, which is of great significance for the protection of origin labeling of products.