The invention relates to a time synchronization method and system for an SDN network of an intelligent substation. The method comprises the following steps: the SDN controller acquires a current clockprovided by the clock source through the SDN controller time synchronization interface and performs time service on the SDN switch, the SDN controller issues a flow table based on the current clock,and the SDN switch acquires the current clock through the SDN switch time synchronization interface and performs time service on the measurement and control device. According to the time synchronization method and system for the SDN network of the intelligent substation, the SDN controller is introduced into the intelligent substation, a traditional Ethernet switch networking mode is replaced, centralized processing of network protocols can be carried out, the operation efficiency and convergence speed of complex protocols can be improved, and the looped network self-healing problem in the substation can be solved.