The invention provides a radix scutellariae flavone phenylpropanoidand and flavonoid O-methyltransferase gene. The radix scutellariae flavone phenylpropanoidand and flavonoid O-methyltransferase genecomprises at least one of SbPFOMT1, SbPFOMT2 and SbPFOMT5 genes, the gene sequence of the SbPFOMT1 is as shown in SEQID No.1, the gene sequence of the SbPFOMT2 is as shown in SEQID No.3, and the genesequence of the SbPFOMT5 is as shown in SEQID No.5; and a primer composition amplifying the gene, protein coded by the gene, a recombinant vector, a recombinant microorganism, a host cell, a transgenic cell line, transgenic plant tissue or a transgenic plant constructed by the gene, and an application of the recombinant vector, the recombinant microorganism, the host cell, the transgenic cell line, the transgenic plant tissue or the transgenic plant are provided. The methylation process of wogonin and similar flavonoid is analyzed, 3 flavone phenylpropanoidand and flavonoid O-methyltransferasegenes SbPFOMT1, SbPFOMT2 and SbPFOMT5 are obtained for the first time and cloned, besides, the function of enzymes coded by the gene is verified in an exogenous plant and a microorganism body, a theoretical basis is provided for methylation of wogonin and similar flavonoid in mass production, and a firm basis is also established for industrial production of other pertinent flavonoid compounds.