A control apparatus for a compressor of a vehicle capable of turning-on/off a compressor based on coolant pressure of an air conditioner in the winter and a method thereof are provided. The control apparatus includes a compressor that is configured to reduce a temperature by compressing a coolant of an air conditioner and a controller that is configured to operate the compressor, to confirm an operation coolant pressure of the air conditioner after operating the compressor. The controller also operates the compressor based on the operation coolant pressure of a measured coolant pressure of the air conditioner when an ambient temperature of the vehicle is less than a reference temperature.