A method was developed for the preparative separation of two alkaloids from the crude extract of the radix of Rauvolfia verticillata (Lour.) Baill. in a single run. The two-phase solvent system composed of petroleum ether–ethyl acetate–methanol–water (5:5:2:8, v/v), where triethylamine (40 mmol/L) was added to the upper organic phase as the stationary phase and hydrochloric acid (10 mmol/L) was added to the lower aqueous phase as the mobile phase, was selected for this separation by pH-zone-refining counter-current chromatography (PZRCCC). For the preparative separation, the apparatus was rotated at a speed 850 rpm, while the mobile phase was pumped into the column at 2 mL/min. As a result, 112 mg of reserpine and 21 mg of yohimbine were obtained from 3 g of crude extract in a single run. The analysis of the isolated compounds was determined by high-performance liquid chromatography (HPLC) at 230 nm with purities of over 91.0%, and the chemical identification was carried out by the data of electrospray ionization–mass spectrometry (ESI–MS) and nuclear magnetic resonance (NMR) spectroscopy. The technique introduced in this paper is an efficient method for preparative separation of reserpine and yohimbine from devil pepper radix. It will be beneficial to utilize medicinal materials and also useful for the separation, purification, and pharmacological study of Chinese herbal ingredients.