The invention discloses a harmless microorganism treatment method for cadavers of livestock and poultry. The method particularly includes the following steps: placing the cadavers in boxes, cutting, separating, crushing and slicing the cadavers, deoiling the sliced meat, fermenting and degrading the deoiled meat, performing high temperature sterilization and preparing a fertilizer, wherein during the fermenting and degrading step, thermophilus spoilage bacterium and mesophilic non-spore bacteria are employed as bacterial strains, wherein the thermophilus spoilage bacterium is composed of one or more selected from bacillus stearothermophilus, Cl.thermosaccharolyticum, clostridium butyricum, streptococcus thermophilus and bacillus macerans; and the mesophilic non-spore bacteria is composed of one or more selected from streptococcus liquefaciens, streptococcus faecalis, byssochlamys fulva, leuconostoc dextranicum, yeast and mildews. The organic fertilizer, by means of the key functions of the microorganisms, can supply various nutrient elements to crops and also can supply large amount of biotins, amino acids, vitamins, growth hormone, antibiotics and the like physiological active components that are necessary in growth of the crops.