The invention discloses a phase modifier emergency control method and a system thereof. The method comprises a step of sending pre-received low-voltage ride-through information to an emergency controlmain station when a new energy unit has low-voltage ride-through and obtaining monitored new energy station bus voltage information and all phase modifier operation information in a power grid, a step of matching a corresponding emergency control measure from a preset control strategy table according to the low-voltage ride-through information, the collected new energy station bus voltage information and the phase modifier operation information and sending the corresponding emergency control measure to a phase modifier control substation, and a step of sending a command of modifying excitation reference voltage and a duration command to a phase modifier excitation system and restoring the excitation reference voltage to an initial value when the duration is ended or an excitation system under-excited or over-excited protection limit is triggered to complete the emergency control of a phase modifier. According to the invention, the new energy chain high-voltage off-grid risk caused bya condition that a large-scale new energy unit enters a low voltage ride-through state is effectively reduced, and the prevention of a chain power outage accident of a new energy high-ratio power gridis facilitated.