Disclosed herein is a two-way motion type active air flap system of a vehicle, which includes first, second, and third air flaps configured by a combination of a row array of air flaps and a column array of air flaps. The column array of air flaps is opened forward in a revolving manner by the rotational force of a flap rotary actuator, and the row array of air flaps is opened laterally in a sliding by the rotational force of a flap sliding actuator, so that the first, second, and third air flaps control a blast space through which external air passes. Thus, since the front opening and the lateral opening of the air flaps are performed independently, it is possible to fundamentally prevent an adverse effect of causing overcooling and deteriorating aerodynamic performance.