Most applications of underwater cyber-physical system (UCPS) demand reliable data collection in an efficient and timely manner. However, the energy-constrained characteristic on acoustic communication makes it challenging to collect data. In this paper, we study the energy-efficient data collection for UCPS over autonomous underwater vehicle (AUV) assisted underwater acoustic sensor network. The sensor nodes perceive local physical parameters, whose lifetime is strictly restricted by local power. The AUV that has relatively sufficient energy is adopted to retrieve data from sensor nodes. To balance energy consumption and prolong underwater network lifetime, the energy optimization problem is formulated as minimizing the sum of edge lengths of a particular graph. Then, a min-weighted rigid graph based topology optimization scheme is developed for sensor deployment. With the optimized network topology, a local routing decision algorithm is developed for each sensor node to relay the collected data to the data collectors (sinks). A dynamic value-based path planning strategy is also designed for the AUV to dynamically visit data collectors to maximize the value of information (VoI) within a given time. Finally, simulation results demonstrate that the network lifetime with the topology optimization scheme can be prolonged, and the dynamic value-based path planning strategy can improve the VoI on AUV.