The taproot of Aconitum carmichaelii Debeaux (AC), a poisonous Traditional Chinese Medicine, has been widely used to treat joint pain, rheumatism and dysmenorrhea. Fermentation is a traditional drug processing method that reduces toxicity or increases efficacy. However, the chemical composition of AC, especially fermented AC, has not been fully elucidated. Therefore, it is necessary to establish a method to characterize the chemical composition of raw and fermented AC. In this study, a structural feature-based comprehensive strategy was employed to identify the chemical components of raw and fermented AC. A highly selective method consisting of mass defect filtering (MDF), ring double bond (RDB), nitrogen rule, and feature MS fragments filtering was established using UPLC-Q-Orbitrap-MS. By the established method, 230 diterpene alkaloids were characterized in raw AC, including 108 amine, 68 monoester, and 54 diester diterpene alkaloids. 145 of them were potential new compounds. Totals of 466 diterpene alkaloids were identified in fermented AC, including 231 amine, 162 monoester, and 73 diester diterpene alkaloids. 397 of them were potential new compounds. Ester hydrolysis, hydroxylation, and demethylation were the major transformation pathways during fermentation. An integrated approach with highly selective based on the structural feature of analytes was established and applied to identify the chemicals in AC. The strategy showed great performance in improving the accuracy and coverage of the identification by using LC-MS.