A method and a system for preventing surge of a vehicle may include: determining whether an engine operation mode is a particulate filter regeneration mode or a catalyst desulfurization mode; determining, when the engine operation mode is the particulate filter regeneration mode or the catalyst desulfurization mode, a torque change; determining whether the torque change is smaller than a predetermined value; determining, when the torque change is smaller than the predetermined value, whether an intake pressure is higher than an exhaust pressure by at least a predetermined pressure; and opening, when the intake pressure is higher than the exhaust pressure by at least the predetermined pressure, an exhaust gas recirculation (EGR) valve and a throttle valve.