Global positioning system (GPS)-disciplined quartz oscillator can provide a precise time and frequency standard. However, possible phase errors and biases caused by oscillator phase noise must be suppressed or compensated for some applications, e.g., distributed radar systems, in which a rigorous phase or frequency synchronization precision is required. Moreover, the quartz oscillator is necessary to provide a holdover of time or frequency when the GPS signals are lost. This letter presents a signal processing and hardware design strategy for suppressing phase noise in GPS-disciplined frequency synchronization systems. Firstly, the quartz oscillator frequency is disciplined by the GPS pulse-per-second (PPS) signals. Next, a recursive algorithm is applied to suppress the possible jitters when the GPS PPS signals are lost. Finally, a direct digital synthesizer (DDS)-based multiple frequency tuning synthesizer is presented to generate the whole system frequencies. Although the use of GPS signal to discipline oscillator for frequency transfer is not a new concept, the originality of this letter lies in the proposed phase noise suppression methods, along with the hardware design strategies.