The invention discloses a preparation method of a microorganism organic fertilizer. The preparation method of the microorganism organic fertilizer comprises the following steps: uniformly mixing excrements of livestocks, rice husk and saw dust, regulating the pH value, and preparing a raw material; adding an anaerobic bacteria into the uniformly mixed raw material, and carrying out anaerobic reaction; adding aerobic bacteria into the raw material after the anaerobic reaction is finished, uniformly mixing, and carrying out aerobic reaction, so that the microorganism fertilizer is obtained. The preparation method of the microorganism organic fertilizer has the advantages that dual fermentation is adopted, the total nutrient of the organic matter and the organic fertilizer can be in a good state, soil and the cultivation soil fertility are improved, soil is cured, nutrients are provided for crops, energy and nutriments are provided for soil microorganisms, microbial activities are promoted, and decomposition of the organic matter is sped up; experiments show that radish planted in a vegetable base adopting the microorganism organic fertilizer is crisp with high moisture content of 2-3% and popular in customers; besides, soil after planting is loose, and great benefit on protection of soil and underground water is realized.