The invention relates to an automatic control system of a bean sprouting box used for a ship. The automatic control system comprises a temperature control module, a humidity control module and a waterspraying module, wherein the temperature control module is used for collecting temperature signals according to temperature sensors, adjusting the temperature through a temperature and humidity controller according to the preset temperature and increasing or decreasing the temperature in the bean sprouting box to the preset temperature, the humidity control module is used for collecting a humidity signal according to a humidity sensor, adjusting the humidity through the temperature and humidity controller according to the preset humidity and increasing or decreasing the humidity in the bean sprouting box to the preset humidity, and the water spraying module is used for receiving a water level signal according to a water level controller, adjusting the water level through a water pump, a water inlet and a water outlet according to a preset water level signal and supplementing water or discharging redundant water until the water level reaches the preset water level. By means of the automatic control system, it is achieved that adjustment of the temperature, the humidity and the water level in the bean sprouting box is intelligently controlled, so that the production cycle of bean sprouts is shortened to 2-3 days.