Navigation equipment phased array antenna is mainly composed of atenna array, phase shifter and control unit. Phase shifter is responsible for real-time phase control of antenna array. In order to eliminate the phase deviation between phasers of navigation equipment phased array antenna, an Fast Fourier Transform (FFT) phase solving technology based on system generator is proposed, and the phase solving model of phaser of navigation equipment phased array antenna is rapidly constructed by system generator to complete the phase solving and compensation work. It has been proved that the method can effectively shorten the programming time of the designer and has strong application value.