The deliberately origin mislabeling of sweet cherry causes significantly disruptions to market integrity and consumers' trust. In this study, 153 cherry samples from five provinces in China and the corresponding irrigation water and soil samples were collected. 5 stable isotope ratios (δ13C, δ15N, δ2H, δ18O, 87Sr/86Sr) and 8 multi-element contents (Na, Mg, P, K, Ca, Fe, Zn, Se) of cherry were determined by EA-IRMS and ICP-MS to study isotopic fractionation and elemental enrichment mechanisms for origin traceability. The results show the δ2H and δ18O of cherry exhibit a strong correlated with its irrigation water (r2 > 0.85), while δ15N, 87Sr/86Sr, Fe, Zn and Se contents are related to its cultivated soil (r2 > 0.75), and the δ13C is related to the local microclimate. ANOVA reveals that the regional differences of δ13C, δ2H, δ18O, 87Sr/86Sr as well as Na, Mg, Ca contents of cherry are significant (P < 0.05), and are important geographical indicators. Various multivariate modeling methods, HCA, PLS-DA, and LDA, were employed with the overall accuracy exceeding 90%. This strategy provides an effective mean to verify the label authenticity of cherry origin in Chinese market.