The present invention discloses a novel microbial medicine fertilizer in the technological field of microbiology and a preparation method thereof. The raw materials that are used for preparing the medicine fertilizer have the following portions: 1 portion of photosynthetic bacteria of 310,000,000 per milliliter, 1 portion of lactic acid bacteria of 420,000,000 per milliliter, 1 portion of acetobacter spp of 180,000,000 per milliliter, 1 portion of yeast of 200,000,000 per milliliter, 1 portion of Gram-positive actinomycete of 150,000,000 per milliliter, 1 portion of filamentous aspergillus of 200,000,000 per milliliter in the system of fermentation, 0.5 portion of rice vinegar, 0.5 portion of white wine, 0.015 portion of azadirachtin, 3 portions of salt and 390 portions of purified water. The novel microbial medicine fertilizer has the advantages of high activity, high stability and fast effect, and has the functions of killing harmful bacteria, killing pests and fertilization. And the microbial medicine fertilizer is non-toxic and conducive to the environmental protection. The preparation method has the advantages of simple process, easy operation, high practicality and suitability for the development of local areas, and fits the national conditions of China and the trend of agricultural development. And the technology has broad application prospects in agriculture, animal husbandry, aquaculture and environmental protection.