Aconitum pendulum N. Busch (Ranunculaceae) is rich in alkaloids with anti-inflammatory and analgesic activities. Many studies have focused on the identification or quantification of alkaloid components using low-throughput tests. However, the metabolic differences of plants from environmentally distinct regions remain unclear. The present study profiled alkaloid chemical compounds in the rhizomes of A. pendulum from different regions. A total of 80 chemical compounds were identified using a widely targeted ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) approach. Principal component, hierarchical clustering, and orthogonal partial least squares-discriminant analyses of the chemical compounds indicated that the plants from 6 regions clearly separated into distinct groups. A total of 19 compounds contributed the most to the metabolite differences between collection areas and were identified as potential metabolic markers. The antiinflammatory activities of the A. pendulum extracts were also evaluated and the potential environmental effects on the regulation of metabolite composition and bioactivity were explored. These results improve our understanding of the variation in chemical composition of plants from different regions and will serve as a reference for evaluating the medicinal value of A. pendulum in different environments.