To address the issues of solid waste accumulation on the walls of aquaculture chambers in factory ships, low efficiency of manual cleaning, and the inability to clean in a timely manner, a cleaning system suitable for the aquaculture chambers of factory ships was designed. This cleaning system, considering the specific characteristics of aquaculture in factory ships, includes a cleaning device, a bypass device, a transmission device, and a sewage discharge system. Through simulation experiments, the optimal operating speed of the system and the cleaning efficiency of the device under different working conditions were determined. The results indicate that the system's operating speed should be kept below 0.5m/s, and the slower the speed, the higher the cleaning efficiency. Increasing the rotational speed of the brush can significantly enhance cleaning efficiency. It was also found that the number of working cycles of the brush per unit path is positively correlated with cleaning efficiency. When the operating speed is 0.2m/s and the brush speed is 190r/min, the cleaning effect is ideal. A 30° angle for the cleaning scraper effectively removes residual attachments. The study shows that this cleaning system can resolve the cleaning issues during the aquaculture process, with a compact and efficient structure, high work efficiency, and cost-effectiveness, making it valuable for broader application.