Cynanchum acutum L. subsp. sibiricum (Willd.) Rech. f. was extracted with hexane, acetone, methanol and water individually. A sample was heated in water then extracted with ethyl acetate. Among the extracts, the ethyl acetate extract exhibited the most antiproliferative activity, so isolation of bioactive compounds was carried out from this extract. A new compound, kaempferol-3-O-β-xylopyranosyl-(1-2)-β-rhamnopyranoside (1) along with five known compounds, quercetin-3-O-β-xyloside (2), kaempferol-3-O-β-glucoside (3), quercetin-3-O-β-glucoside (4), kaempferol-3-O-β-rhamnopyranoside (5), and kaempferol-3-O-β-d-neohesperidoside (6) were isolated from ethyl acetate extract. The structures were elucidated by spectroscopic techniques, basically 1D NMR, 2D NMR and LC-TOF/MS. Antiproliferative effects of isolated compounds were determined by xCELLigence using the HeLa (human uterus carcinoma) cell lines. Compound 2 and compound 5 revealed the good antiproliferative activity against HeLa cell lines.