The invention discloses a moving target defense system for an SDN (self-defending network). The system consists of a moving target defense module and an SDN controller management module; the moving target defense module comprises a flow analysis module, a mapping information storage module, a target conversion module, an encryption transmission module, a load balance module, a safety authentication module, a business flow recording database and a mapping information recording database; the SDN controller management module comprises a flow table generation module, a flow table distribution/synchronization module, a route selection module, a DNS service module, a load balance module, a distributed management module, a safety communication module, a redundant backup module, a safety authentication module and a flow table database; furthermore, the invention also discloses a moving target defense method for the SDN. Through the moving target defense system and the moving target defense method disclosed by the invention, the difficulty of an attacker to detect a target is increased further, and therefore the safety of an intranet is comprehensively protected.