A device and a method for a controlling compressor of vehicles improves acceleration performance and fuel efficiency and maintains comfort of a cabin by decreasing an operation of the compressor when accelerating. The device may include a sensor module including a cabin temperature sensor, an outdoor temperature sensor, an evaporator temperature sensor detecting a temperature of a cooling medium in an evaporator, an engine speed sensor detecting rotation speed of an engine, and a throttle position sensor detecting a throttle opening, an air conditioning system including a condenser condensing and liquefying the cooling medium, an evaporator evaporating the liquefied cooling medium, the compressor compressing the cooling medium, a temperature control door controlling a temperature of an air flowed in a cabin, an intake door selectively flowing an inner air or an outer air in the cabin, and a blower blowing the air to the intake door, and a controller controlling an operation of the air conditioning system, wherein the controller decides a acceleration mode and an allowable temperature at each acceleration mode when an acceleration condition occurs, and decreases an operation of the compressor according to a difference between the evaporator temperature and the allowable temperature.