Because azimuth and elevation difference channels are not orthogonal in monopulse angle tracking system, this paper presents a new digital phase calibration method by using two NCOs to compensate the azimuth and elevation phase differences to reduce the error of angle estimation with indepth study of the angle error extraction principle in I/Q processor. With an analysis of the precision of angle tracking under different calibration methods, the feasibility of the new method can be validated. As a simulation result, the precision of dualchannel monopulse angle tracking system can be improved.