Disclosed are a method of and an apparatus for controlling a vibration of a hybrid electric vehicle. An apparatus for controlling a vibration of a hybrid electric vehicle may include: an engine position detector detecting a position of an engine; an air amount detector detecting an air amount flowing into the engine; an accelerator pedal position detector detecting a position of an accelerator pedal; a vehicle speed detector detecting a speed of the hybrid electric vehicle; an SOC detector detecting a state of charge (SOC) of a battery; and a controller controlling operation of a motor based on the position of the engine, the air amount, the position of the accelerator pedal, the speed of the hybrid electric vehicle, and the SOC of the battery.