Underwater acoustic network (UAN) is a lightweight system used in inland waterway systems. Software-defined networking (SDN) is a promising approach to improve the supervision abilities and integration services. This paper introduces SM-UAN, an SDN-based UAN with multi-controllers. Firstly, a hierarchical framework of SM-UAN is offered. Secondly, a multi-flow table structure and a multi-flow processing method is built. Followed by, a distributed deployment model of controllers and a load balancing mechanism are established. Finally, we construct an experimental scenario on Mininet with WOSS-NS3. The simulation demonstrates that the compression ratio is promoted to 24.1%, the compression ratio 29.4%, the packet forwarding rate 14.7% and the processing delay 31.2%, when comparing SM-UAN with the item-by-item matching (IM) system. For the load balancing mechanism, it shows that the maximum load for a master controller is balanced to 0.55, while the minimum load for a slave controller 0.46, which proves that a fair load distribution achieves. In addition, SM-UAN is compared with the traditional single-sink-based UAN (TS-UAN), the traditional multi-sink-based UAN (TM-UAN), and the SDN-based UAN with a single controller (SS-UAN). The results reveal that the survival time of SM-UAN is extended to 32.7%, 24.9%, and 21.6%, respectively. Also, the bit error rate (BER) of that is less than 10-4. In conclusion, advantages of SM-UAN have been highlighted, which provides theoretical support for inland waterway systems.