The invention provides a protective ecological dredging method of river lake and wetland integral transplantation. The method comprises the following steps that mesh division is performed on an excavation region of a river lake and a wetland, the excavation region is divided into n grid units; meanwhile, the excavation region is precisely positioned and layered, the upper layer is an ecological layer, and the lower layer is a sludge layer; the ecological layer and the sludge layer of the grid unit at the first position are removed to form a first blank grid unit; the sludge layer of the grid unit at the second position is removed and moved to the first blank grid unit, the sludge layer of the grid unit at the second position is removed, and a second blank grid unit is formed; and the ecological layer of the grid unit at the third position is removed and moved to the second blank grid unit, the sludge layer of the third position grid unit is removed, and a third blank grid unit is formed. According to the method, the ecological layer of the grid unit at the Nth position is removed and moved to the N-1th blank grid unit, the sludge layer of the N position grid unit is removed, and integrated protective ecological sludge removing for the river lake and the wetland is realized.