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The separation of minor compounds, especially those with similar polarities from a complex sample, remains challenging. In the proposed study, an effective method based on medium-pressure liquid chromatography and recycling high-speed counter-current chromatography was developed for the enrichment and separation of three minor components from <i>Dracocephalum tanguticum</i>. The crude extract was directly introduced to medium-pressure liquid chromatography for the enrichment of the three minor components. Based on high-performance liquid chromatography analysis, the total content of these three compounds increased from 0.48% in the crude extract to 85.3% in the medium-pressure liquid chromatography fraction. In addition, high-speed counter-current chromatography was employed to separate the enriched compounds using the solvent system hexane/ethyl acetate/methanol/water (1.18:8.82:1.18:8.82, v/v/v/v). As a result, compound <b>3</b> and a mixture of compounds <b>1</b> and <b>2</b> were obtained. In order to improve the resolution of compounds <b>1</b> and <b>2</b> while saving separation time, a recycling and heart-cut mode was used. Finally, compounds <b>1</b> and <b>2</b> were obtained after five cycles. These compounds were identified as 3-phenylethyl β-d-glucopyranoside (<b>1</b>), tazettoside E (<b>2</b>), and cirsiliol-4′-glucoside (<b>3</b>). Compounds <b>1</b> and <b>2</b> were primarily separated from <i>D. tanguticum</i>. Moreover, the developed method provided a reference for the separation of minor components from the complex sample.