The invention discloses a preparation method of a microbial agent capable of continuously desilting and removing a black and odorous water body. The preparation method comprises the following steps: adding mineral powder for planting into soil for planting green leaf plants, collecting grown green leaf plants, mixing the collected green leaf plants with sterile purified water, crushing and stirring a mixture to obtain a plant culture medium; preparing the following raw materials in parts by weight: 10.2 to 36.0 parts of the mineral powder with 100 to 300 meshes for culturing, 0.5 to 5.5 parts of the plant culture medium, 0.3 to 2.5 parts of plant source microorganisms and 56.0 to 89.0 parts of the sterile purified water for culturing; preparing microbial liquid from the raw materials, fusing the microbial liquid with to-be-treated plant source microbial liquid obtained by collecting and domesticating in an original river branch according to the weight part ratio being 3:7, and finally, mixing a mixed solution with broken ore grains to obtain a finished product. The microbial agent disclosed by the invention can realize instant settlement for taking effect, quick field planting and propagation expanding at the bottom of a river bed and continuous biological deodorization, desilting and water purification within 3 to 6 months, is ecological and environment-friendly, and is suitable for treating the black and odorous water body in the river branch.