The invention discloses an automatic control ultrasonic bean seedling breeding device and a bean seedling breeding method thereof. The automatic control ultrasonic bean seedling breeding device comprises a planting shed, planting pots, a movable light shield, an ultrasonic atomizer, a temperature controller and a timer, the planting pots, the movable light shield, the ultrasonic atomizer, the temperature controller and the timer are arranged in the planting shed, the temperature controller is arranged on the light shield, so that the temperature in the light shield is adjusted, the timer is electrically connected with the ultrasonic atomizer, so that on/off of the ultrasonic atomizer is controlled in a timing manner, fertilizers dissolved in water are atomized by the aid of the ultrasonic atomizer and uniformly sprayed on bean seeds in the planting pots, efficient absorption is facilitated in the production process of bean seedlings, humidity in the air is increased, temperature environments suitable for growth of the bean seedlings are controlled, growth of the bean seedlings can be facilitated, and production efficiency is improved. According to the bean seedling breeding method by controlling the ultrasonic atomizer in a timing manner, excellent bean seeds are firstly selected and soaked, operating time of the ultrasonic atomizer is controlled in a timing manner, suitable temperature environments are controlled, and the bean seedlings are optimally produced.