A minor lignan, 4'-demethyldeoxypodophyllotoxin, was isolated from Sinopodophyllum emodi. First, a crude extract of S. emodi was analyzed by high performance liquid chromatography-mass spectrometry (HPLC-MS) to confirm the presence of the target compound. Then, the target lignan was successfully enriched in the crude extract precipitate by medium-pressure LC (MPLC) with high recovery (85%). Finally, an efficient separation was achieved by high-speed counter-current chromatography (HSCCC) using a two-phase solvent system of n-hexane-ethyl acetate-methanol-water (1:1:1:1, v/v/v/v). These results clearly demonstrate that the combination of HPLC-MS, MPLC, and HSCCC could be a powerful technique for the rapid screening, enrichment, and separation of minor compounds from complex natural products.