OBJECTIVE：To virtually screen lignanoid compounds with inhibitory effect of histone deacetylase（HDAC）by virtual screening method. METHODS：Using“lignanoid”as keyword，requiring CNKI，VIP，PubMed and other database，lignanoid compounds were collected as ligand to establish ligand base，histone deacetylase receptor HDAC2 （PDB code：4LXZ） and HDAC8（PDB code：1T69）were selected from PDB database，and then ligands and 3D active site of receptors were docked by SYBYL-X 2.0 software. The affinity of receptors to ligand was reflected by total score. RESULTS：345 lignanoid compounds， 4LXZ and 1T69 primary ligand were used to establish ligand base which included 347 ligands. Ligands No.275，271，110，200， 056，258，181，129，037，270，187 were demonstrated good affinity with receptors HDAC2 and HDAC8. Ligands and receptors residue were docked via hydrogen bond. CONCLUSIONS：Lignanoid compounds have inhibitory effect on HDAC；virtual screening method is effective in natural product activity prediction，which can provide quick access to and theoretical guidance for new pharmacological studies of lignanoid compounds.