The invention belongs to the field of fertilizer, and particularly relates to a three-resistant compound microbial fertilizer and a preparation method thereof. The three-resistant compound microbial fertilizer is prepared from plenty, medium and trace elements nitrogen, phosphorus, potassium, compound fertilizer, paraffin, associated nitrogen fixing bacteria, phosphorus solubilizing bacteria, potassium solubilizing bacteria and bacillus such as brevibacillus laterosporus, bacillus cereus, bacillus subtilis and bacillus licheniformis by compounding. The molten liquid paraffin is used for enveloping, and the molten paraffin doped with complex microbial inoculants is used for secondary enveloping. In the invention, live microbial products are added into the conventional compound fertilizer and provide direct or indirect nutrient elements to the plants through the movement of the microbial inoculants, while improving the soil fertility, activating the soil, enhancing the stress resistance of the crops, and solving the problems of soil fertility reduction, soil hardening, nutrient unbalance and lack of stress resistance of the crops; moreover, the invention has long period of validity, resists high temperature, acid-base and dryness, is nontoxic and harmless to people and livestock, and can prevent and control pests, deal with the pieces of paddy field without lodging and obviously increase the yield.