The invention discloses a hydraulic drive device of an underwater gate valve. The hydraulic drive device comprises an upper valve cover assembly, an elastic part, a leather bag, a valve rod and a piston, the upper valve cover assembly is fixedly connected with the top end of a valve body to form a cavity, the piston is movably connected with the inner wall of the upper valve cover assembly to divide the cavity into a first cavity and a second cavity, the elastic part and the leather bag are contained in the first cavity, the upper valve cover assembly is provided with a hydraulic in-out port communicated with the second cavity, a liquid injection hole communicated with the first cavity and an inflation hole communicated with an inner cavity of the leather bag, one end of the valve rod is fixedly connected with the piston, and the other end of the valve rod is fixedly connected with the top end of a flashboard to drive the flashboard to move relative to a valve base assembly. The invention further discloses the underwater gate valve and the control method of the underwater gate valve. According to the hydraulic drive device, due to the protection function of the upper valve cover assembly, the leather bag can be made of common materials to meet pressure compensation requirements.