Rheum tanguticum is one of the primary rhubarb species used for food and medicinal purposes, and it has recently been gaining more attention and recognition. This research represents the first attempt to use stable isotopes and elemental analysis via IRMS to identify the geographical origin of Rheum tanguticum. A grand total of 190 rhubarb samples were gathered from 38 locations spread throughout the provinces of Gansu, Sichuan, and Qinghai in China. The carbon content showed a decreasing trend in the order of Qinghai, followed by Sichuan, and then Gansu. Nitrogen content was notably higher, with Qinghai and Sichuan displaying similar levels, while Gansu had the lowest nitrogen levels. Significant differences were noted in the δ13C (−28.9 to −26.5‰), δ15N (2.6 to 5.6‰), δ2H (−120.0 to −89.3‰), and δ18O (16.0‰ to 18.8‰) isotopes among the various rhubarb cultivation areas. A significant negative correlation was found between %C and both longitude and humidity. Additionally, δ13C and δ15N isotopes were negatively correlated with longitude, and δ15N showed a negative correlation with humidity as well. δ2H and δ18O isotopes exhibited a strong positive correlation with latitude, while significant negative correlations were observed between δ2H and δ18O isotopes and temperature, precipitation, and humidity. The LDA, PLS-DA, and k-NN models all exhibited strong classification performance in both the training and validation sets, achieving accuracy rates between 82.1% and 91.7%. The combination of stable isotopes, elemental analysis, and chemometrics provides a reliable and efficient discriminant model for accurately determining the geographical origin of R. tanguticum in different regions. In the future, the approach will aid in identifying the geographical origin and efficacy of rhubarb in other studies.