Abstract: The content of 3, 6′-disinapoy sucrose, tenuifoliside C and 3′-O-(E)-3, 4, 5-trimethoxycinnamoyl-β-D-fructofuranosyl-(2→1)-(6-O-benzoyl)- α-D-glucopyranoside in root of the 3 species of Polygala japonica, P.lijiangensis and P.wattersii were determined by HPLC. Results show that the contents of 3 sucrose esters were higher in the roots than the whole plant both in the 3 plants of Polygala. The contents of 3, 6′-disinapoy sucrose reached to 8.32 mg/g and 6.52 mg/g in the roots of P.japonica and P.lijiangensis, higher than the medicinal provisions which did not allowed less than 5 mg/g in the Chinese Pharmacopoeia. The study provides basis for the medicinal value and the reference for the development and utilization of Polygala.