Objective: The use of microwave digestion coupled with inductively coupled plasma mass spectrometry (ICP-MS) to measure the content of metal elements in Citrus Medica L. var. sarcodactylis from different regions serves as a reference for tracing its origin and provides a basis for quality control and safety assessment of its heavy metal content. Methods: After microwave digestion of Citrus Medica samples, metal element contents from different regions were determined using ICP-MS, with methodological investigations conducted. A diverse statistical analysis was performed to explore the relationship between geographical distribution of Citrus Medica and metal element contents. Additionally, safety assessments were conducted using single factor pollution index and Nemerow comprehensive pollution index methods for several heavy metal elements. Results: The contents of elements such as Mg, Fe, and Al are relatively high in Citrus Medica. Characteristic differences in elements like Al, Ni, Mg, Cr, Sr, and Zn among samples from different regions are evident. Principal component analysis (PCA) indicates that samples from Sichuan Province can be clustered by origin. Elements including Ni, Co, Al, As, Cu, and Fe may contribute significantly to distinguishing Citrus Medica from different regions. Pollution assessments for several heavy metals conclude that Citrus Medica samples are safe and clean. Conclusion: The ICP-MS method is rapid and accurate, capable of simultaneous measurement of multiple metal elements in Citrus Medica. Combined with multivariate statistical analysis, it facilitates origin tracing studies of Citrus Medica from various regions, particularly enabling effective differentiation of those from Sichuan Province.