Abstract: An active sonar system of a fish finder can transmit the ultrasonic waves into the water below, and receive the returning echoes from the objects underwater in the fishing industry. The conventional fish finder can search only vertically underneath the own ship. By contrast, the multi-beam fishing sonar is the typical device to search both horizontally and vertically underwater using sound waves in the pelagic fish finder. The underwater transducer can be used to transmit and receive acoustic signals underwater. Among them, the multi-beam fishing sonar host is the core hardware of the fishing sonar system, due mainly to its high technical performance, integration, stability, and reliability. Furthermore, the detection of marine organisms can depend directly on the thermal design, one of the key technologies of sonar hosts in the whole system. In this study, a series of designs and verification was carried out for the efficient heat dissipation of multi-beam fishing sonar hosts for ocean operation. The heat dissipation analysis of the sonar host for fishing was also implemented to realize the thermal design of the sonar host for fishing, according to the relevant theories of heat transfer and structural design. Firstly, the heat dissipation mode was determined to fully meet the industrial requirements of the airtight performance of the sonar host, according to the structure design of the sonar host and various heat dissipation. Specifically, natural cooling was used for the shell of the host and the external environment, whereas, forced air cooling was adopted for the interior of the host. A systematic analysis was then made to determine the structure of the sonar host for fishing. The heat dissipation was also analyzed during the entire process from the heat source to the board, the chassis, and the external environment. As such, some suggestions were proposed in the whole process of design and manufacture. Secondly, the thermal simulation software was used to simulate the heat dissipation process of the sonar host. Four schemes were compared to optimize the design of the air duct after simulation. An optimal design scheme was selected from the four air ducts after comparison. At the same time, an optimal cooling fan was obtained with a simple structure after simulation, according to the cooling requirements of industrial design. The impact of various cooling fans was evaluated on the thermal stability of the host at ambient temperatures of 20, 30, 40, and 50°C. More importantly, the higher the temperature was, the worse the thermal stability of the host was. A comparison was performed on the temperature distribution before and after the thermal design of the sonar host, indicating the excellent effectiveness of the thermal design of the sonar host. Finally, the field test of heat dissipation was conducted to further verify the overall performance of heat dissipation in the host. Meanwhile, the temperature was measured on the eight FPGA boards. The results show that the thermal design scheme effectively controlled the temperature rise inside the host. The thermal design of the fishing sonar host greatly improved the heat dissipation capacity and heat accumulation. Consequently, the thermal stability of the equipment can be expected to provide for the design and manufacturing process of the multi-beam fishing sonar host. The reason was that a low thermal resistance channel was formed between the heat source and the external environment of the host during the simulation and test of heat dissipation. Anyway, the thermal design of the fishing sonar host was considered the installation requirements of the internal structure of the sonar host, particularly suitable for space utilization and heat dissipation in practice. The finding can also provide a strong reference for the structural design of the multi-beam fishing sonar host in the fish finder.