This paper introduces the overall layout of the Free Electron Laser & High Magnetic Field device under construction at Anhui University, and analyzes in detail the design requirements and difficulties in development of the water-cooling system for stable operation of the device, and presents the design of the water-cooling system for the whole device. The water-cooling system contains two independent water-cooling unit systems, with the design temperatures of (42±0.1)℃ and (25±0.5)℃ respectively, which can be adjusted within a certain range. The device water-cooling control system is developed based on EPICS (Experimental Physics and Industrial Control System) framework, the temperature regulation control function is realized by PLC (Programmable Logic Controller) program, and the PID (Proportion Integration Differentiation) parameter configuration is realized by PID regulator. The software development of the control system is mainly to realize the setting of the device parameters and the reading back of the status data under the EPICS environment, and to store the historical data into the Archiver Appliances database. The temperature control accuracy of the water-cooling control system during the trial operation reaches (42±0.03)℃ and (25±0.08)℃, which is in line with the design requirements, and the system is stable and reliable during the operation, which can well guarantee the safe and stable operation of the device.