The invention discloses a preparation method of an organic microbial fertilizer. The organic microbial fertilizer comprises by weight, 26-35 parts of livestock and poultry night soil, 13-18 parts of sweet potato flour, 10-17 parts of wheat middling, 25-40 parts of straws, 30-40 parts of peat soil, 25-35 parts of weathered coal, 10-15 parts of mushrooms, 10-15 parts of algae, 12-16 parts of freshwater mussel powder, 20-30 parts of wood chips, 5-10 parts of honey, 1-2 parts of composite vitamins, 1-3 parts of composite amino acids, 5-8 parts of potassium polymetaphosphate, 1-2 parts of trace elements, 7-13 parts of potassium mineral powder, 10-16 parts of phosphate rock powder, 1-2 parts of humic acid, 5-8 parts of ammonium sulfate, 12-15 parts of borax, 3-7 parts of zinc sulfate, 5-8 parts of sodium carbonate and 7-10 parts of fatty acid acetic anhydride. The preparation method well solves the disadvantages of long fermentation period, and short viability time, activity insufficiency and difficult preservation of bacterial strains, The organic microbial fertilizer meets nutrition required by growth of crops, improves soil environment, has two purposes, and well promotes the sustainable healthy development of Chinese agriculture production.