With the rapid development of network technology and popularity of virtualization, the importance of developing an adaptive management system for such physical and virtual network environment is obvious increasing. Not simply do the demand systems keep the convenience of virtualization, but conform to the hierarchy of system administration. This article presents the Multilayer Virtual Network Management System, integrated the architecture of network virtualization and the features of multilayer network management. The system is implemented by Net FPGA network development platform and provides a solution of network management for a large scale network. Experiments demonstrate the exact execution of Virtual Network through the policies of network flows and the multilayer management of the proposed system.