Variations in optical fiber length and refractive index are induced by environmental perturbation, resulting in an additional dynamic propagation delay in fiber-based time synchronization systems, which deteriorate their transfer stability. This disadvantage can be significantly reduced by transmitting the time signal in both directions through fiber and constructing a feedback loop to compensate the propagation delay at the remote end of the link. This paper proposes an analog-digital hybrid proportional integral derivative (PID) control compensation system based on the time-frequency phase-locked loop (TF-PLL). The system is designed to keep the merits of wide servo bandwidth, servo accuracy, and a large dynamic delay compensation range up to 1 s, which is much greater than that reported in previous studies. For proving the validity of this proposed scheme, a self-developed optical fiber time synchronization equipment based on the delay compensation system is applied. The delay compensation system is used on a 1100-km long laboratory optical fiber, and the results show that the time synchronization stability in terms of time deviation (TDEV) is less than 5.92 ps/1 s and 2.56 ps/10,000 s. After successful laboratory evaluation, the proposed system is installed on a real 988.48-km line between the Xi’an Lintong branch of the National Time Service Center (NTSC) and Linfen City, Shanxi Province, realizing the time synchronization of 10 stations along the optical fiber link. The experimental results in the 988.48-km link illustrate that the measured time difference with a peak-to-peak value of 176 ps, the standard deviation of 19.3 ps, and a TDEV of less than 10.49 ps/1 s and 2.31 ps/40,000 s is achieved. The high-precision time delay compensation system proposed in this paper is simple, reliable, and accurate; has a wide range of compensation; and opens up a feasible scheme for providing synchronized time signals to multiple users over the long-distance field optical fiber networks.