The invention discloses a comprehensive organism repairing method of an eutrophication seawater cage culture zone, which is characterized by comprising the following steps of: hanging large-scale seaweeds on the upper part of a water body in a cage culture zone by using immobilized microorganisms, the large-scale seaweeds and filter-feeding bivalves as a combined repairing organism; putting the filter-feeding bivalves capable of rapidly absorbing and converting inorganic nitrogen and phosphorus eutrophication substances in the water body to the bottom of the culture zone; putting the immobilized microorganisms partially depositing to the surface layer of a bottom material of a culture field; and intensifying the degradation of organic matters and the nitrification velocity of nitrogen in the water body or substrate sludge through the oxidization and the nitrification. The method has the characteristics that firstly, the comprehensive organism repairing method which uses the large-scale seaweeds, the filter-feeding bivalves and immobilized nitrobacteria as a main organism can eliminate the eutrophication substances and organic pollutants in the water body and the bottom material; and secondly, the large-scale seaweeds and the filter-feeding bivalves with higher economic value can be obtained while eliminating the pollutants, thereby great environment and economic benefits are achieved.