High-speed countercurrent chromatography (HSCCC) and silica gel column chromatography were used to separate and purify alkaloids from Chinese herbal medicine Euchresta tubulosa Dunn. The purpose of this study is to provide a system mode for rapid separation of alkaloids from natural products. In the experiment, the eluent of silica gel column chromatography was screened by thin layer chromatography (TLC) to obtain four components with different polarity. Then, the two-phase solvent systems of different components were selected and purified by HSCCC. Four alkaloids with relatively high content were obtained by this mode successfully, including matrine (28 mg), oxymatrine (32 mg), N-formyl cytisine (24 mg), and cytisine (58 mg). The purity was higher than 91% by high performance liquid chromatography−ultraviolet (HPLC-UV) and their chemical structures were identified by nuclear magnetic resonance (NMR) and electron ionization mass spectrometry (EI-MS). The results showed that the combination of HSCCC and silica gel column chromatography could make alkaloids from natural products separate systematically.