An apparatus for controlling a compressor includes a stroke calculator for calculating a stroke estimate value of a compressor based on a value of a current applied to a motor of the compressor and a value of a voltage applied to the motor of the compressor; an operation frequency reference determining unit for integrating the stroke estimate value to output an integrated stroke value, detecting a mechanical resonance frequency of the compressor based on the integrated stroke estimate value and the current value, and determining the detected mechanical resonance frequency as an operation frequency reference value; and a controller for varying a current operation frequency of the compressor according to the determined operation frequency reference value.