Underwater long-distance wireless communication (ULWC) is a critical challenge in many applications, such as marine environmental monitoring, underwater remote control, and underwater navigation, to name a few. However, very little literature focuses on ULWC, especially where the communication distance ups to thousands of kilometers, which is urgently required in the underwater Internet of Things (UIoT) in the large-scale and deep sea. In this paper, to improve the underwater communication capacity at a level of thousands of kilometers, we propose a three-hop underwater wireless acoustic communication (3H-UWAC) structure based on the Sound Fixing and Ranging (SOFAR) channel. The proposed 3H-UWAC consists of transmitters, relay stations (RSs), and receivers. Different from the existing ULWC, 3H-ULWC can improve energy efficiency with a small vertical directivity angle (VDA). Due to the characteristics of UWAC, the straight-line communication link can be realized in the proposed three hops, and the communication distance can be increased to thousands of kilometers. Respecting the randomness of underwater devices, tools from stochastic geometry are used to model the spatial distributions of transmitters’, receivers’, and RSs’ locations. RSs are set on the SOFAR channel at a known depth. In the first hop, the transmitter sends information to the nearest first relay station (NFRS) on the SOFAR plane. In the second hop, the NFRS sends information to the nearest relay station, which is called the nearest second relay station (NSRS), to the receiver on the SOFAR plane. In the third hop, SNFS sends information to the receiver. All three communication hops can be achieved with a narrow beam width, where the energy efficiency is improved critically. With given densities of transmitters, RSs, and receivers, the coverage probabilities (CPs) of the three hops (transmitter to FRS, FRS to SRS, and SRS to receiver) are analyzed, and the final CP from a transmitter to a receiver through the 3H link is derived. Insights about the effects of VDAs at the transmitters, FNRS, and SNRS, as well as the depths of transmitters and receivers, are revealed. A rapid optimization method is proposed based on the analytical results. The accuracy of the analysis is verified by Monte-Carlo simulations.