The invention discloses a control system for an automatic water drain valve of a fuel filter, and relates to the technical field of water drain devices of automobile fuel systems. The control system comprises a signal acquisition and control module, a water level detection module, a temperature detection module and a water drain valve drive module, wherein the water level detection module is located in a water accumulation cup of the filter, connected with a signal input end of the signal acquisition and control module, and used for detecting water level information in the water accumulation cup; the temperature detection module is located on the automatic water drain valve, connected with the signal input end of the signal acquisition and control module, and used for detecting environment temperature information; and a control signal output end of the signal acquisition and control module is connected with a control end of the water drain valve through the water drain valve drive module. The system controls the automatic water drain valve according to an environment temperature, the water level information and a water drain time simultaneously, and is high in control accuracy and good in use effect.