Abstract:Flavivirus infection causes severe human disease, but no specific drugs are available to treat flavivirus infection. The N terminal region of non-structural protein 3 (NS3) of flavivirus and its cofactor NS2B constitute protease, and the polyprotein produced by virus is cleaved by protease into structural and non-structural proteins that are essential for the replication of the virus. NS2B-NS3pro represents an attractive drug target due to its critical role in the life cycle of flavivirus. Here we review the structural advances of NS2B-NS3pro of Zika Virus, Dengue Virus and West Nile Virus as well as the complex structures of some protease with inhibitors, these will provide necessary references for the future antiviral drug design.