Rapid characterization of chemical analogues in potentially toxic complex matrix was essential for prevention of accidental poisoning. On the basis of the fragment ions possessed not only the same retention times (RT) but the same drift times (DT) on liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS), an alternating frames (AF)-data independent acquisition (DIA) was utilized for simultaneous detection and rapid match of precursor/product ions with a fast switch of low/high collision energy (CE). A diagnostic ions guided 2D-locating strategy was developed for identification of chemical analogues in potentially toxic herbal medicines using LC-IM-MS. Firstly, the 2D-locations (RT, DT) of diagnostic ions were screened from high-fragment IM-MS frames according to their m/z. Then, the correlated precursor ions were extracted from the complex background interference in low-fragment IM-MS frames based on diagnostic ions' 2D-locations. Finally, the remained ions were characterized using double-bond equivalent analysis combined with MS/MS fragment interpretation. Totally, 236 diterpene alkaloids including eight compounds with potential new esterification types were characterized in processed lateral roots of Aconitum carmichaelii Debx. Moreover, the LC-IM-MS distribution regularities of diterpene alkaloids with various chemical structure types were further investigated and discussed. This study presented an innovative idea for revealing the chemical basis related to the toxicities of potentially poisonous herbal medicines to ensure the medication safety.