The invention relates to a cutter-suction packing pumping method for cleaning contaminated sediments in a river, which is characterized in that: the sediments are conveyed to a hydraulic separation tank by using a cutter-suction dredger, and the left coarse particles after screening are mechanically transported to a dump to be treated; liquid fine particles self-flows into a treatment pond and are packed and sealed from the top of the treatment pond by using a closed device; a water filtering system is arranged in the sealed body, a water filtering layer capable of adsorbing heavy metal ions is arranged at the bottom of the water filtering system, a pond bottom pipe network which is communicated with the water filtering layer is arranged in the sealed body, and a pumping passage is arranged in the water filtering layer; the gas-water mixture in the sealed body is forcibly absorbed from the pumping passage by using a jet pumping and water adsorbing device until the liquid fine particles are converted into a solid state from a liquid state; the solid fine particles are mechanically transported to a centralized stacking spot; and tail water is treated by using a chemical reagent and discharged into the river after meeting the emission standard. The method has the advantages of no diffusion of pollution because the mud water body is isolated from the outside in the treatment process, no derivative, less power consumption, high efficiency and environmental-friendly treatment of underwater contaminated sediments.