OBJECTIVE To find the best synthesis method of 6-benzyl-1-[(benzyloxy)methyl]-3-hydroxy-5-(hydroxymethyl) pyrimidine-2,4(1H,3H)-dione e for observing the change of its biological activity after N-3 hydroxylation. METHODS After trying some N-hydroxylation methods, the target compound was successfully synthesized via one-pot oxidizing process by sodium hydride (NaH) and 3-chloroperbenzoic acid(m-CPBA); the anti-HIV reverse transcriptase (RT) activity and integrase (IN) activity of the target compound was assayed via enzyme-linked immunesorbent assay (ELISA) and phosphorylation of DNA package method. RESULTS The target compound could be obtained through the improved m-CPBA oxidative method by only one step, and the yield of the reaction could reach 60%-70%. And the structure of this compound was identified by 1H NMR, 13C NMR and MS; The activity result showed it added the anti-HIV IN activity after N-3 hydroxylation as well as retained the anti-HIV RT activity. CONCLUSIONS The improved m-CPBA oxidative method is a convenient and efficient way to prepare the compound 6-benzyl-1-[(benzyloxy)methyl]-3-hydroxy-5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione e which has both anti-HIV RT and IN activity.