The invention discloses a multifunctional base modifier and a preparation method thereof. The multifunctional bottom modifier includes: peanut shell powder, peanut antimicrobial peptide, peanut water-soluble dietary fiber, tea polysaccharide, diatomaceous earth, xanthan gum, cerium ammonium nitrate, zeolite powder, Bacillus pumilus, Bacillus subtilis, swamp red Pseudomonas, Lactobacillus plantarum, Saccharomyces cerevisiae. Preparation method: cerium ammonium nitrate and xanthan gum are catalyzed by microwaves to make xanthan gum polysaccharide-cerium complex; mix it with diatomite, Bacillus pumilus, Bacillus subtilis, Rhodopseudomonas palustris, Lactobacillus plantarum , beer yeast to make microcapsule preparation; peanut shell powder, peanut antibacterial peptide, peanut water-soluble dietary fiber, tea polysaccharide, microcapsule preparation and zeolite powder are mixed and granulated. The multi-functional bottom modifier has the functions of adsorbing heavy metals, degrading pesticide residues and drug residues, resisting harmful bacteria and viruses, degrading organic matter, reducing the concentration of ammonia nitrogen, nitrite, and hydrogen sulfide in water and bottom, improving bottom quality, and improving water transparency. Function.