The invention discloses a gate underwater opening/closing device for assisting fish migration and upstream going and an opening/closing method based on the gate underwater opening/closing device for assisting the fish migration and upstream going, and relates to the technical field of gate opening/closing. The gate underwater opening/closing device for assisting the fish migration and upstream going comprises a power line, an electric lifting rod, a water sealing seat and square steel, wherein the power line is connected with an external control system, and conveys power required by a driving motor of the electric lifting rod; the driving motor drives a ball screw to rotate in a nut through a reduction gear unit; and the ball screw converts rotary motion into linear motion of the nut to push a push rod to rise and open a gate. The water sealing seat comprises round steel, an oil seal and bolts; the outer sides of the electric lifting rod and the water sealing seat are sleeved and connected with the square steel, and the water sealing seat and the square steel prevent water leakage of the electric lifting rod. According to the invention, waterproof measures are improved, the common electric lifting rod opens and closes the gate underwater, the underwater opening/closing method can prevent a hydraulic jump phenomenon under the gate, and hydrodynamic conditions beneficial to the fish migration and upstream going are formed.