To investigate the chemical constituents of the roots of Polygala wattersiiHance,the separation and purification were performed by solvent extraction and repeated column chromatography (CC) on silica gel, Sephadex LH-20 and macroporous resin D101, preparative TLC and semi-preparative HPLC. The structures were identified by spectroscopic analysis and comparison of their1H and 13C NMR data with those reported in literatures. Twenty-three known compounds, including eleven xanthones (1-11), nine sugar esters (12–20), two triterpenoid saponins (21 and 22) and one phenylpropanoid (23) were isolated and their structures were identified as 1,3-dihydroxyxanthone (1), 1-hydroxy-3-methoxyxanthone (2), 1,3-dihydroxy-2-methoxyxanthone (3), 1,3,7-trihydroxy-2-methoxyxanthone (4), 1,3,6-trihydroxy-2,7-dimethoxyxanthone (5), 1,6,7-trihydroxy-2,3-dimethoxyxanthone (6), 1,7-dihydroxy-2,3-methylenedioxyxanthone (7), 1,7-dimethoxyxanthone (8), 1,2,3-trimethoxyxanthone (9), 1-methoxy-2,3-methylenedioxyxanthone (10), 6-hydroxy-1-methoxy-2,3-methylenedioxyxanthone (11), 3'-O-feruloyl-6-O-acetyl sucrose (12), arillatose B (13), sibricose A5 (14), sibricose A6 (15), 3',6-di-O-sinapoyl sucrose (16), tenufoliside A (17), 3'-O-3,4,5-trimethoxycinnamoyl-6-O-p-methoxybenzoyl sucrose (18), glomeratose A (19), 1-O-p-coumaroyl-D-glucopyranose (20), bayogenin-3-O-glucoside (21), tenufolin (22), and sinapic acid (23). Among them, compounds 2 and 12 were obtained from genus Polygala for the first time, and except compound 16, all others were isolated from this species for the first time.