The invention discloses an underwater material dredging system comprising a water control center, a desilting system, a slag conveying system and an underwater robot, the desilting system, the slag conveying system and the underwater robot are all connected with the water control center, the desilting system is fixedly connected with the slag conveying system, the desilting system comprises a mudsuction device, a water spraying device and a monitoring device which are all connected with the water control center, the mud suction device is fixedly connected with the slag conveying system, and the water spraying device and the monitoring device are both connected with the mud suction device. The invention further comprises a dredging method of the underwater material dredging system. The underwater material dredging system and the dredging method solve the problems that in the prior art, the actual dredging point of an underwater material is difficult to accurately position, the dredgingeffect is poor, the cost input is large, pipe damage or the suction difficulty in the large particle size material suction process is generated, the dredging difficulty is large, and the dredging efficiency is low.