Abstract: For large scale underwater sensor networks, the characteristics of underwater acoustic channel are investigated. A static beacon node based clock synchronization algorithm is presented for the nodes inside the beacon nodes coverage area, and a dynamic node assisted clock synchronization algorithm is designed for the nodes outside the beacon nodes coverage area. These methods reduce the effect of node mobility. A layering clock synchronization mechanism based on the feature of underwater sound velocity is proposed, which solves the clock synchronization problem of large scale underwater sensor networks. The simulation results show that, the proposed synchronization method is obviously better than existing algorithms.