Most of the existing UWSNs clock synchronization algorithms use nodes to exchange data frequently, but neglect the synchronization information received by neighbor nodes within the scope of node-based communication, so there are some problems such as high energy consumption and low synchronization efficiency in synchronization communication, which affect the accuracy of network clock synchronization. Therefore, based on the analysis of the influence of UWSNs multi-objective optimization network topology evolution process on clock synchronization, this paper uses the theory of group consistency and Markov chain to establish the synchronization cycle regulation mechanism and clock synchronization model without too much increase of the average transmission radius and communication energy consumption. Then, using linear regression fitting method, the inter-cluster synchronization and intra-cluster synchronization are established. Finally, the performance of UWSNs clock synchronization algorithm is verified by simulation.