The invention provides a microbial composite organic fertilizer for preventing and controlling wheat scab, and a preparation method thereof. The microbial composite organic fertilizer comprises a microbial composite bacterial agent and an organic waste according to a weight ratio of (4-8):(2-6), wherein the microbial composite bacterial agent comprises Trichoderma harzianum, Bacillus subtilis, Lactobacillus and yeast, and based on the weight of the microbial composite organic fertilizer, the effective viable count of Trichoderma harzianum is not less than 300 million cfu / g, the effective viable cell count of Bacillus subtilis is not less than 500 million cfu / g, the effective viable cell count of Lactobacillus is not less than 300 million cfu / g, and the effective viable cell count of yeastis not less than 300 million cfu / g. According to the present invention, with the microbial composite organic fertilizer, the disease resistance of wheat is significantly improved; and the production process is simple, the strain is easy to culture, the method is suitable for large-scale production, and a certain social and economic benefit can be achieved.