The present disclosure provides an O-methyltransferase protein with a highly specific catalytic function for multiple benzylisoquinoline alkaloids (BIAs) parent nuclei and an encoding gene and use thereof. Compared with wild-type O-methyltransferase, the O-methyltransferase protein (SEQ ID NO: 2) shows an enhanced enzymatic activity and a wider substrate scope. The O-methyltransferase protein can catalyze O-methylation of backbones from three BIAs, including monobenzylisoquinolines (norcoclaurine, coclaurine, and N-methylcoclaurine), aporphines (asimilobine and N-methylasimilobine), and protoberberines (scoulerine and tetrahydrocolumbamine). Meanwhile, this O-methyltransferase protein is highly regioselective for each backbone. The O-methyltransferase protein catalyzes methylation of the monobenzylisoquinolines at 6-OH and 7-OH, is only active on 6-OH of the backbone of the aporphines, and mainly catalyzes methylation of the protoberberines at 2-OH. Moreover, the O-methyltransferase protein has a stronger catalytic activity and can be used as a biocatalyst for the semi-synthesis of related compounds.