The invention provides a configuration method and system for quickly deploying SDN networking through dual virtualization, and the method comprises the following steps: S1, building an overlay virtualnetwork, configuring a test script on an overlay virtualization platform, and carrying out the initialization of SDN networking; S2, the configuration test script is managed and issued through SDN API configuration data, and the management data is issued to a database of an overlay virtualization platform; S3, setting a management node of the SDN API running on the overlay virtualization platform, configuring the management node to adopt dual-computer virtualization deployment, and setting main and standby dual-computer data synchronization; S4, configuring a new-server component to obtain management data issued to the overlay virtualization platform database by the SDN API, and performing operations of adding a switch, a network and a sub-network to complete configuration of SND networking.