The invention discloses a preparation method of a slow release fertilizer for schoenoplectus trigueter with a high fertilizer utilization rate. The preparation method comprises the following steps of:mixing whey protein, polymaleic acid, polyethylene glycol and water, carrying out heating, stirring, and heating again, continuously stirring the mixture, carrying out spray drying, adding microcrystalline cellulose and oxidized starch, and uniformly stirring the mixture to obtain a material a; mixing sodium selenite, gypsum powder, wollastonite powder, manganese humate and hexaurea ferric trinitrate, adding water, and stirring the materials uniformly to obtain a first prefabricated material; mixing puffed blood powder, pig manure and sunflower seed meal uniformly, and adding compound fermenting bacteria for fermentation to obtain material c; and adding the first prefabricated material, urea, ammonium sulfate, calcium superphosphate and a potassium magnesium salt into the material c, uniformly mixing the materials, granulating the mixture, spraying the material a for coating to obtain the slow release fertilizer for schoenoplectus trigueter with a high fertilizer utilization rate. Thefertilizer obtained by the method provided by the invention has an extremely high utilization rate of nutrient substances and a slow nutrient substance loss speed, and can improve the quality of schoenoplectus trigueter, enhance the stress resistance of schoenoplectus trigueter, reduce the risk of agricultural environment pollution and protect the environment.