A three-phase solvent system was efficiently applied for high-speed counter-current chromatography to separate secondary metabolites with a wide range of hydrophobicity in Dicranostigma leptopodum. The three-phase solvent system of n-hexane/methyl tert-butyl ether/acetonitrile/0.5% triethylamine (2:2:3:2, v/v/v/v) was selected for high-speed counter-current chromatography separation. The separation was initiated by filling the column with a mixture of intermediate phase and lower phase as a stationary phase followed by elution with upper phase to separate the hydrophobic compounds. Then the mobile phase was switched to the intermediate phase to elute the moderately hydrophobic compounds, and finally the polar compounds still retained in the column were fractionated by eluting the column with the lower phase. In this research, 12 peaks were eluted out in one-step operation within 110 min, among them, eight compounds with acceptable purity were obtained and identified. The purities of β-sitosterol, protopine, allocryptopine, isocorydione, isocorydine, coptisine, berberrubine, and berberine were 94.7, 96.5, 97.9, 86.6, 98.9, 97.6, 95.7, and 92.8%, respectively.