The present invention discloses an apparatus and method for controlling a linear compressor (43) which can actively handle load and efficiently perform an operation, by synchronizing an operation frequency with a natural frequency of a movable member varied by the load. The apparatus for controlling the linear compressor includes a counter electromotive force phase detecting unit (45) for detecting a phase of a counter electromotive force from a voltage command value of the linear compressor (43) and an input current, a current phase detecting unit (46) for detecting a phase of the input current, a frequency generating unit (47) for comparing the phase of the counter electromotive force with the phase of the input current, and generating a frequency change value, a control unit (48) for correcting the voltage command value according to the frequency change value, and an inverter unit (42) for receiving a direct current voltage, generating a sine wave voltage according to the corrected voltage command value, and applying the sine wave voltage to the linear compressor (43).