The invention belongs to the technical field of the rail wagon, and particularly relates to a grain hopper car and a control system thereof. The grain hopper car comprises a hopper car box. The top of the hopper car box is provided with a small top cover and a large top cover respectively. The small top cover and the large top cover are respectively connected with a top cover open-close air cylinder installed at two sides of the hopper car box by a long shaft. The end part of the hopper car box is provided with an end door. The end door is connected with an end door connecting rod. The end door connecting rod is connected with an end door transmission shaft. The end door transmission shaft is connected with an end door open-close air cylinder. The bottom of the hopper car box is provided with a bottom door I and a bottom door II. The bottom door I and the bottom door II are respectively connected with a bottom door open-close air cylinder I and a bottom door open-close air cylinder II by a bottom door connecting rod. Each of two sides of the grain hopper car is provided with a control box. The respective or linked control of six power sources in the open-close system can be realized at any one side of the hopper box by an operator through the connection of a pipeline and a flow valve.