An active vibration reduction control apparatus and method of a hybrid vehicle are provided to generate a reference signal of a first motor that corresponds a vibration signal extracted from a second motor. An amplitude and phase of the reference signal is adjusted based on frequency characteristic of a drive system transfer function to generate vibration reduction torque of a first motor within the hybrid vehicle. The first motor, a torsional damper, an engine, a connector (a belt-pulley, a chain, a gear, and so on), and the second motor are sequentially connected within the hybrid vehicle.