The invention discloses an error matrix compensation method of a monopulse tracking receiver system, relating to compensation for system errors in a two-dimensional self-tracking system in the field of communication. The method comprises the following steps: analyzing the reason causing the error of the tracking receiver system; obtaining a system error compensation matrix through formula deduction; measuring and analyzing a large amount of test data to determine specific parameters of the compensation matrix; and finally introducing the compensation matrix into a ground digital tracking receiver to eliminate the system error. The method has the characteristics that the equipment is simple, the use and maintenance are convenient, the performance is stable and reliable and the like; and the method is especially suitable for a two-dimensional tracking receiver in a measurement and control system for the measurement and control of unmanned aerial vehicle and the like.