The invention provides a fault crossing control method and a system of a doubly-fed wind turbine generator system, comprising the following steps of: collecting the terminal voltage of the doubly-fedwind turbine generator system; According to the terminal voltage and the preset threshold, the doubly-fed wind turbine generator system enters the preset fault crossing control mode or the normal control mode. The fault ride-through control mode includes determining the rotor control voltage of the doubly fed wind turbine generator system according to the phase jump value of the terminal voltage.The fault crossing control mode provided by the method and the system takes the dynamic influence of the voltage phase into consideration, does not affect the stable operation state of the system, effectively improves the accuracy of the unit control when the terminal voltage phase jumps, and ensures the fault crossing of the doubly-fed wind turbine unit.