An optical fiber is a promising approach for data and clock transmission in distributed underwater sonar systems. However, synchronization is a critical challenge in distributed sonar systems, which mandates accurate clock synchronization down to a sub degree. Potential phase misalignment is caused by fiber length variations. In this paper, we propose a fiber-based phase stabilizer method to achieve accurate clock synchronization among sensor nodes. We use fiber-based feedback loop between sensor nodes and central station unit to monitor phase variations. Subsequently, we leverage phase shifters symmetrically arranged on the forward lane and feedback lane to compensate real-time phase variation and maintain high-precision synchronization. Besides, an ambiguity eliminator circuit is designed to remove the clock’s cyclic ambiguity. Both analysis and experimental results suggest that the proposed phase stabilizer can achieve 10 MHz reference clock synchronization within 0.4 degree. We also analyze the impact of the reference clock’s phase error on the system range detection accuracy, which indicates that the proposed phase stabilizer can greatly improve detection accuracy of sonar systems.