An apparatus for reducing vibrations of a two-cylinder engine for a hybrid electric vehicle includes a reference signal generator for generating a first reference signal and a first reference phase, a speed calculator for calculating a speed of the motor based on the position of the motor, a vibration extractor for extracting a first vibration signal based on the speed of the motor, a variable filter, a filter coefficient updater, a phase calculator, a phase shift compensator, a synchronization signal generator for generating a first synchronization signal synchronized with the first vibration signal based on a first reference phase transferred from the reference signal generator, the second phase difference transferred from the phase calculator and the first compensation value transferred from the phase shift compensator, an inverse phase signal generator, and a torque generator for generating a final command torque based on the first inverse phase signal.