Aconitum pendulum Busch is rich C19 diterpenoid alkaloids, but there is no report of imidazole alkaloid in Aconitum pendulum Busch. In this study, an imidazole alkaloid named 1H-imidazole-2-carboxylic acid, butyl ester (ICABE) was successfully separated from Aconitum pendulum Busch with semi-preparative high-speed counter-current chromatography (HSCCC). The partition coefficient was measured by HPLC to select the solvent systems for ICABE separation by HSCCC. The separation was performed with a two-phase solvent system composed of n-hexane-chloroform-ethanol-water (10:1 : 13:2, v/v/v/v). The upper phase was used as the stationary phase and the lower phase as the mobile phase. It was operated at a flow rate of 1.8 mL/min. The apparatus was rotated at 850 r/min, and the detection wavelength was set at 230 nm. Under the selected conditions, a high efficiency separation of HSCCC was achieved, and 7.5 mg of ICABE was obtained from 100 mg of the crude sample of Aconitum pendulum in one-step separation within 350 min. The HPLC analysis showed that the purity of the compound was over 98%. The chemical structure was confirmed by UV, 1H-NMR and 13C-NMR. The established method is simple, highly efficient and suitable for large scale separation of ICABE from radix of Aconitum pendulum Busch.