System and method for controlling compressor of vehicle

A system for controlling a compressor may include an engine controller controlling a fuel injection amount corresponding to an engine load and an opening amount of a throttle by reflecting a required torque required for an air conditioner, an operation information detector for detecting operation information according to driving state of the vehicle, a compressor generating pressure through a piston operation of a cylinder utilizing the power of the engine during operation of the air conditioner, and a controller determining an engine negative pressure of an intake manifold stored in the brake booster at a value, and when the negative pressure of intake manifold is below a first threshold value when the brake is operated, the engine enters a negative pressure recovery mode for predicting an insignificant negative pressure drop condition that falls below a second threshold value which is the A/C cut control condition and reduces the A/C duty.