Euchresta tubulosa Dunn. is a Chinese herbal medicine with biological activity, but there are few studies on its components at present. Alkaloids in the stem of Euchresta tubulosa Dunn. were isolated and purified by high-speed counter-current chromatography (HSCCC) using stepwise elution. First of all, liquid-liquid extraction (methylene chloride-methanol-water, 5:1:4, v/v) was used for the preliminary enrichment. According to the partition coefficient (K) of a target compound in a series of different two-phase solvents, the final result was that carbon tetrachloride-methylene chloride-methanol-water (2:3:3:2, v/v) (1) and methylene chloride-methanol-water (5:3:2, v/v) (2) were suitable for the HSCCC using stepwise elution. As a result, the purity was all higher than 93% and matrine (1), oxymatrine (2), N-formyl cytisine (3), and N-acetyl cytisine (4) can be eluted at one time by this mode. Cytisine-type alkaloids were isolated for the first time in this plant. Finally, the applicability of the mode was verified.