Time synchronization is the basis of coordination and cooperation in underwater acoustic networks. However, because of the propagation delay, node mobility, and Doppler shift, it is impossible to balance the accuracy and energy consumption simply in water. As a promising technology, partial clustering has high convergence and makes breakthroughs in time synchronization. This paper proposes PCDE-Sync, a novel synchronization mechanism with partial clustering and the Doppler effect. Firstly, a clustering method built on the artificial fish swarm algorithm is presented. It models the cluster construction according to fish's preying, swarming, and following behaviors. Secondly, we design a synchronization mechanism to conduct clock correction and compensation by the Doppler effect. Finally, we compare the performance of PCDE-Sync with the most advanced protocols, namely MU-Sync, MM-Sync, and DE-Sync, in terms of the cumulative error after synchronization, the mean square error under different clock skew and that under distinctive node mobility, and energy consumption. The experimental results show that PCDE-Sync makes a trade-off between accuracy and complexity, which does well in solving synchronization issues.