The invention relates to a preparation method of a microbial organic fertilizer for fruit trees. The microbial organic fertilizer is prepared by steps of preparing a decomposed product from biogas residue, straw and herbal residues as raw materials and fermenting by stirring the decomposed product and a bacteria liquor mixture. The organic fertilizer contains complete nutrient elements, can improve soil, improve physical and chemical properties of the soil, enhance water retention, fertilizer maintenance and fertilizer supply abilities of the soil. In addition, the organic fertilizer also canenhance product quality, improve rhizosphere micropopulation of crops, raise pest and disease resistance of plants, promote utilization of fertilizers and increase utilization rate of fertilizers, enhance soil porosity, permeability and survival rate of plants, and increase beneficial bacteria and soil microorganisms and populations. Meanwhile, predominant beneficial microflora formed at the rootsystem of crops can inhibit the proliferation of harmful pathogens, enhance stress resistance and disease resistance of crops, and reduce disease index of replanted crops. By continuous application ofthe organic fertilizer, successive cropping obstacle can be greatly alleviated, and the environmental pollution can be reduced. The microbial organic fertilizer is safe and nontoxic to human, livestock and the environment, and is an environmentally-friendly fertilizer.