Shanghai Chongming rice wine was used as the main research subject in this study. The natural abundance of hydrogen and oxygen stable isotopes (δ²H and δ¹⁸O values), mineral elements and free amino acids content were analyzed. The discriminant models of Chongming rice wines were established and the characteristic variables were screened by principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). The results showed that the δ²H and δ¹⁸O values, mineral elements and free amino acids content in rice wines from different geographic origins were different, but only δ²H and δ¹⁸O values and the content of Ca and Mn were statistically significant (P ＜0.05). The principal component analysis could realize the geographical origin discrimination of Chongming rice wines. The accuracy of the optimal model of PLS-DA for Chongming rice wines was 100%. Based on variable importance for the projection, eight variables including δ²H, Sr, Arg, Mn, Cu, Zn, Ca and δ¹⁸O were identified as the characteristic variables of Chongming rice wine for geographic origins discrimination. The results can be applied to the geographical traceability of rice wine.