Aconitum pendulum, a member of the Aconitum genus within the Ranunculaceae family, is known for its remarkable anti-inflammatory, anti-tumor, and analgesic properties. However, the application of Aconitum pendulum in traditional medicine is often restricted by its inherent toxicity, necessitating specific processing methods to ensure safe usage. Tibetan medicine utilizes distinctive processing techniques such as the barley wine, Hezitang, and zanba frying systems to render the herb safe for medicinal use. Despite the known pharmacological importance, scant research exists on how these processing methods affect the phytochemical profile of Aconitum pendulum, indicating a necessity for comparative analysis of the resulting concoctions. In this study, we employed( 1)H nuclear magnetic resonance (H-1 NMR) spectroscopy and ultra-performance liquid chromatography coupled with quadrupole time of flight mass spectrometry (UPLC-Q-TOF-MS) to explore the metabolomic variations among different processed products of Aconitum pendulum. Multivariate data analysis techniques, including pattern recognition, allowed us to investigate the intricacies of the compound profiles. To discover signature chemical markers that can differentiate the various processed products, we conducted paired t-tests and generated heat maps highlighting the detected differences. Our integrated analysis of the H-1 NMR and UPLC-Q-TOF-MS data revealed distinct chemical signatures unique to each method of Aconitum pendulum processing. By employing chemometric analysis with variable importance in projection (VIP) scores greater than 1.0, and coupled with the statistical rigor of paired t-tests (P < 0.05), we successfully identified significant chemical markers in various processed products, including ferulic acid (FA), caffeic acid (CA), 3-acetylaconitine (AAC) and benzoylaconitine (BAC). Our findings provide a rapid and robust analysis of the chemical constituencies within raw and processed Aconitum pendulum. The discovery of potential chemical markers through an array of advanced pattern recognition techniques offers a substantial contribution to the pharmaceutical analysis. The results of this research pave the way for future comparative studies and facilitate the recognition of distinctively processed Aconitum pendulum products in traditional medicine.