Aucklandiae Radix (AR) and Vlanimiriae Radix (VR), as traditional Chinese medicine, have been included in many editions of Chinese Pharmacopoeia with similar efficacy such as promoting qi and relieving pain, which often used to treat chest, hypochondriac, abdominal fullness and pain, diarrhea and tenesmus. In most conditions, VR was used to be a substitute of AR or a local habit. However, whether VR could substitute for AR to play a same role in the formulation and clinical applications needed further study.In this study, similarities and differences between AR and VR would be assessed, and possible reasons that may influence the efficacy of the AR and VR would be explained from the perspective of chemical composition.HPLC-PAD was used to obtain the data of 10 batches of AR and VR, and to establish chemical fingerprint and chemometric analysis. UPLC-ESI-Q-TOF-MS was used to identify the structure of chemical ingredients.The chemical fingerprint results showed that 10 batches of AR and VR had a good similarity (>0.9) with 20 and 26 common chromatographic peaks respectively, and 20 batches of samples with 15 common chromatographic peaks also presented a good similarity (>0.9). Nevertheless, chemometric showed AR was distinct from VR and three chemical constituents, which leading to their differences, were identified by UPLC-ESI-Q-TOF-MS. The three chemical constituents were 3β-acetoxy-11β-guaia-4 (15), 10 (14)-diene-12,6α-olide, 10α,14-epoxy-11β-guaia-4 (15)-ene-12,6α-olide and costunolide, respectively.In general, AR and VR were highly similar, but their differences were deserved to attention, were existed among them. This research could provide reference for quality control and set a foundation for clinical applications of AR and VR.