An operation controlling apparatus for a reciprocating compressor, and a method thereof, which are capable of accurately controlling the reciprocating compressor by sensing a size of a load applied to the reciprocating compressor and a stroke estimation value of the reciprocating compressor and then compensating a parameter of a motor in the reciprocating compressor based upon the sensing, the operation controlling apparatus comprising a controlling unit a controlling unit for comparing a phase difference between a detected current and a stroke with a reference phase difference to determine a size of a load, and outputting, according to the determined size of the load, a compensation control signal to compensate a parameter of a motor and a stroke control signal to control the stroke.