In recent years, fiber-based frequency dissemination has attracted widespread attention. A phase-locked loop (PLL) on the transmitter side (TX) is used to compensate for the phase noise caused by the environmental disturbance (PNE). However, the phase noise caused by transfer delay (PNT) cannot be suppressed. A clean PLL on the receiver side (RX) is used to improve the phase noise of the received signal. Consequently, the performance of PLLs on both sides significantly impacts the phase noise of the final recovered signal. The empirical configurations of PLL parameters often fail to achieve optimal results. In this article, a phase noise control method is proposed and demonstrated. Through analyzing the PNT, PNE, and phase noise margin of the recovered signal, we optimally configure the PLL parameters at the TX and RX. In this way, the PNT is effectively suppressed, and the compensation capability for the PNE is evaluated. By comparing the anthropogenic noise in different environments and the compensation capability of the system, this analysis can provide a reference for the construction of large-scale time-frequency networks.