The invention relates to the technical field of river treatment, in particular to a method for polluted river comprehensive treatment. According to the method for polluted river comprehensive treatment, comprehensive treatment is conducted in four aspects including external-source polluted water, river polluted water, river sludge and river periphery. The external-source polluted water and the river polluted water are purified in the method that a compound nanometer water quality conditioner and a compound microorganism preparation are directly added to the external-source polluted water and the river polluted water. One layer of bottom sludge kept constantly at the bottom of a river is beneficial to recovery of the self cleaning capacity of a body of water, after partial clearing is conducted for multiple times, the constant ecological balance of water streams of the river can be achieved, and virtuous cycle can be achieved; artificial landscape balances a wet land and imitates the nature, the conditions beneficial to growth of needed animals are created, and the functions of the soil improvement, water purification, pollution prevention and treatment, automatic balancing of acid rain pollution are achieved. According to the treated river, the water is clear and green all year round, submerged aquatic plants, floating aquatic plants, emerged aquatic plants and the like and animals reappear, the purposes of 'the clear water, the smooth river, the green bank and the beautiful scene' are achieved, and reestablishment of an ecosystem is really achieved.