This invention discloses a recombinant microbial agent of a functional organic fertilizer and the preparation method thereof. The agent is mainly composed of bacillus subtilis, streptomyces jingyamsis, Lactobacillus bulgaricus, Bacillus cereus, bacillus megaterium and Enterococcus faecalis. The prepartation process comprises: bacterium preservation, plate inoculation, shake flask culture of seed solution, 20L seed fermentator culture, 500L fermentator production, centrifuging to collect the thallus, adding protective agent, emulsifying, lyophilizing, disintegrating, active bacteria counting, bacterial compability, vacuum-packing, low temperature storage at -20deg C, and sale for use.The invention is characterized in that, it can prevent and long-term control diseases and pests of fruits and vegetables, improve the quality of fruits and vegetables, and can efficiently resotre and keep the soil ecological balance.