The invention discloses an efficient long-distance dredging method for an underground culvert and a dredging system thereof.The dredging system adopts a control algorithm constructed by the slurry concentration and the motor rotating speed, adjusts the motor rotating speed in real time according to the current slurry concentration, and comprises an underwater dredging robot, a transfer station and a control device; the desilting robot comprises a walking device, a desilting device arranged at the front end of the walking device, a power device used for providing power, a cooling device used for cooling the desilting device and the power device, and a sensing device in signal connection with the control device. By means of the mode, the dredging device is simple in structure, the maximum dredging distance is increased by arranging the transfer station, the rotating speed of the motor is adjusted in time according to the slurry concentration monitored on line, therefore, automatic variable-speed adjustment is achieved, it is ensured that dredging work is conducted smoothly, and the working efficiency is high and the working state is stable through the automatic control mode.