Abstract: OBJECTIVE To provide support for proper medication by researching Pinellia Rhizoma and Typhonii Flagelliformi Rhizoma based on proteomics technology. METHODS Pinellia Rhizoma and Typhonii Flagelliformi Rhizoma were subjected to enzymatic hydrolysis, peptide separation and mass spectrometry data collection were performed by nanoliter liquid phase mass spectrometry, and data processing was performed using protein comparison software. RESULTS The two polypeptide profiles were similar to each other, and there were strong absorption peaks near 14, 19, 52 and 55 min, and the chromatograms of the two peptides were significantly different around 32 and 43 min. There were 1 346 kinds of polypeptides in Pinellia Rhizoma, and 312 species more in Pinellia Rhizoma than in Typhonii Flagelliformi Rhizoma. About 296 kinds of polypeptides were the same in Pinellia Rhizoma and Typhonii Flagelliformi Rhizoma, the same polypeptides were 22% and 29% of the total species respectively. Nine of the top 10 proteins were the same, and they were mainly lectin proteins, but the relative contents were significantly different. CONCLUSION There are significant differences in the kinds and relative contents of the main polypeptides and proteins between them, Typhonii Flagelliformi Rhizoma could not replace Pinellia Rhizoma blindly in clinical practice.