The invention discloses a method for utilizing microorganism in-situ circulation cultivation to treat water body pollution, (1) riverway sewage is utilized to be in-situ cultured, circulated, acclimatized and separated microorganisms out in a culture tank and an biological generator for being put into a water body, and the water body pollution is removed through microorganism absorption, decomposition and transfer; (2) an aerating device is adopted to aerate and provide a good environment for the culture tank, the biological generator and the riverway water body; and (3) a mixer is adopted to stir water sediment, so the pollutant of the sediment enters the water to be utilized by the microorganisms, and the ecological dredging is realized. The invention further discloses a device which is adopted by the method. The method takes nutrients in the reverway sewage as a strain medium, the microorganism environment is improved through aeration and stirring, the added foreign bacterium is more applicable to the water body, is mass propagated and has strong decomposition capacity, so the excellent speed is improved, the source is stable, the purposes of high efficiency, continuity, thoroughness and low cost are realized, meanwhile, the device has strong movability, is convenient to install and dismantle, and has a wide application scope.