The invention provides a method for controlling a water cooling system, and belongs to the technical field of fluid control. The upper computer used in the water cooling system control method comprises a programmable controller with a Modbus communication function, the programmable controller is connected with a water cooling system panel; the water cooling system control method comprises an automatic control mode. The automatic control mode comprises the following steps: a. The water cooling system detects the temperature and pressure of the fluid from the water cooling system to the heatingelement in real time, and the temperature and pressure of the fluid from the heating element to the water cooling system; d. According to the detected fluid temperature from the water cooling system to the heating element, comparing with the preset temperature parameter of the radiating fan, if the detected fluid temperature from the water cooling system to the heating element is higher than the preset temperature parameter, open the three-way ball valve and start the radiating fan. The method strengthens the communication between the host computer and the water cooling system, and can realizeremote control and on-site unmanned duty. It is very suitable for unmanned control occasions similar to wind power generation.