The invention discloses a microbial dredging device, comprising a casing body. The top of the casing body is fixedly connected with a shell, and the top of the casing body is fixedly connected with adriving motor inside the shell. The microorganism is placed in the inner part of the box through the coordination of a driving motor, a driving shaft, a first gear, a rolling bearing, a rotating shaft, a second gear, a controller, a thread sleeve, a thread groove, a threaded rod, a box, a telescopic rod, a drill bit, a cylinder, a through groove and a baffle plate. The controller drives the driving shaft forward or backward by controlling the driving motor, the driving shaft drives the second gear to rotate through the first gear, and the second gear drives the thread sleeve to rotate throughthe rotating shaft. Due to the screw principle, the threaded rod drives the box to move upward or downward, and the microorganism can be applied to the mud at different depth positions. The speed of sludge removal is accelerated, and the sludge removal effect is ideal, which brings great convenience to the dredging work.