Puerarin-7-O-fructoside was transformed by Trichoderma harzianum CGMCC 1523 into 3'-hydroxypuerarin-7-O-fructoside; this was identified by MS and NMR. However, puerarin-7-O-glucoside was not directly hydroxylated but hydrolyzed back into puerarin, which was transformed into 3'-hydroxypuerarin by the same fungi. Comparative analysis of free radical scavenging activity of DPPH showed that the free radical scavenging activity of puerarin-7-O-glucoside was reduced to approximately 1/2 of that of puerarin, while the free radical scavenging activity of puerarin-7-O-fructoside was increased to approximately 1.5 times of that of puerarin. The free radical scavenging activity of 3'-hydroxypuerarin-7-O-fructoside was further increased by 2.2 times of that of puerarin-7-O-fructoside, which was close to that of 3'-hydroxypuerarin.