The invention discloses a deepwater sediment quick discharging system based on pneumatic sediment discharging and a method thereof. The deepwater sediment quick discharging system comprises a compression air source, a sediment discharging mechanism and a control system and is characterized in that an air compressor is arranged in the compression air source, the air compressor is connected with a gas storage tank and is connected with the sediment discharging mechanism through a gas valve switch and a connecting pipeline, and the sediment discharging mechanism comprises an underwater sediment flushing pneumatic discharging part and interface equipment thereof. The control system comprises a control computer, the underwater sediment flushing pneumatic discharging part and an output signal ofa sensor in the interface equipment thereof are connected with the control computer, and an output instruction of the control computer is connected with the compression air source through an executor. The system and method are used for reservoir river and water engineering ship lock lower approach hydraulic draining buildings, and tide gate under-brake channel way sediment rapid conveying transfer, river channel way and Hydraulic engineering draining building clay warp sediment sedimentation can be reduced and prevented, and particularly, the obvious effect on fine sediment is achieved.