The invention relates to a biological disease-preventing organic fertilizer and a preparation method thereof. The components in part by mass of raw materials of the fertilizer are: 65 to 85 parts of decomposed organic substances, 5 to 15 parts of trichoderma bacterial agents, 5 to 15 parts of actinomycetes fermentation broth, wherein the decomposed organic substances are obtained by taking 45 to 65 parts of furfural residue, 20 to 35 parts of cigarette residue and 8 to 20 parts of weathered coal as raw materials, adding 1 to 2 parts of microbial fermentation bacterial agents for stacking fermentation and airing the obtained product till the moisture content is between 25 and 35 percent. The biological disease-preventing organic fertilizer has the advantages of good disease-preventing effect, safety, environment-protecting property and low cost.