The invention discloses an enzyme microbial organic fertilizer and a preparation method thereof. The enzyme microbial organic fertilizer comprises the following components of 40t of fowl manure, 14t of pig manure, 5t of albumen powder, 5t of Chinese wood oil, 10t of peat, 15t of straw powder, 3t of urea, 5t of monoammonium phosphate, 2t of potassium sulfate, 1t of enzyme element expanding agent, 0.2t of rice bran, 0.2t of red sugar and 0.1t of trace elements. The enzyme microbial organic fertilizer can ensure high natural soil building active bacteria, is used for loosening the soil, forms a crumble structure for achieving the effect of remaining water and fertilizing soil, improves the soil, ensures that the root system of crops is developed, can increase the yield and the income, improves the quality of the crops, and is a prophase guarantee of the sustainable development ecological agriculture. Meanwhile, the enzyme microbial organic fertilizer is suitable for a base fertilizer or additional fertilizer of various crops, fruits and vegetables, has remarkable effects of lowering the plant diseases and insect pests and resisting the droop, and is an ecotype environmental-friendly fertilizer for producing organic foods.