An anti-jamming apparatus and method for a compact array antenna are provided. The anti-jamming apparatus for a compact array antenna includes a Global Navigation Satellite System (GNSS) array antenna unit including a plurality of GNSS antennas for receiving GNSS signals transmitted from a satellite. A first beam-forming unit includes a plurality of combination units for receiving respective signals received by the plurality of GNSS antennas as a first reference signal and first auxiliary signals and combining the first reference signal with the first auxiliary signals, thus forming different beams. A second beam-forming unit receives signals of the different beams, and combining the signals of the different beams, thus forming an anti-jamming beam in which an invisible area is minimized.