In this paper, we suggest decoupling control method based on general PI control law to control variable speed refrigeration system of the ship effectively. In the variable speed refrigeration system, the capacity and the superheat are controlled by inverters and electronic expansion valves respectively for saving energy and improving cost performance. Thus, we propose decoupling model to eliminate the interfering loop between capacity and superheat at first. Next, we design PI controller to control capacity and superheat independently and simultaneously. Finally the control performance was investigated through some experiments. The experimental results show that the PI control design can obtain good control performance under the adjustable control reference and thermal load variation.