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 (delta C-13, delta N-15, delta H-2, delta O-18, Sr-87/Sr-86) 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 delta H-2 and delta O-18 of cherry exhibit a strong correlated with its irrigation water (r(2) > 0.85), while delta N-15, Sr-87/Sr-86, Fe, Zn and Se contents are related to its cultivated soil (r(2) > 0.75), and the delta C-13 is related to the local microclimate. ANOVA reveals that the regional differences of delta C-13, delta H-2, delta O-18, Sr-87/Sr-86 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.