The present invention relates to an apparatus and method for controlling operation of a reciprocating compressor. The operating efficiency of the compressor can be improved by performing the steps of: detecting a current and a stroke applied a compressor; a calculating a mechanical resonance frequency by using the detected current and stroke; and determining an operating frequency command value by adding or subtracting the present operating frequency so as to be within a predetermined range of the calculated mechanical resonance frequency and then driving the compressor by the operating frequency command value.