Four naphtolic glycosides (1–4), three anthraquinones (5–7), two stilbenes (8-9), one benzyl glycoside (10), and one flavonoid (11) were isolated from the roots of Fallopia multiflora. The new compounds were elucidated to be 6-hydroxymusizin 8-O-α-D-apiofuranosyl-(1→6)-β-D-glucopyranoside (1) and 6-methoxy-3-methyl-1,6,8-trihydroxy-2-naphthoic acid 8-O-β-D-glucopyranoside (3). Compound 3 could be an important marker for chemotaxonomy of F. multiflora. Benzyl gentiobioside (10) was isolated for the first time from the family Polygonaceae.