The invention discloses a disease controlling microbial fertilizer special for tuberous crops and a preparation method thereof, in particular to a microbial fertilizer special for controlling sweet potato black rot and a preparation method thereof. The microbial fertilizer is prepared by mixing of the following raw materials: antimycoin streptomyces powder, wet streptomyces powder, paenibacillus pabuli powder, paenibacillus jamilae powder, and potassium fulvate raw powder. The strains involved in the invention can utilize the antibiosis, competition, hyperparasitism and bacteriolysis effects between or within microbial species, or utilize secondary metabolites to induce disease resistance of sweet potatoes, and can produce a variety of antibiotics like endomycin compound, non-polyene antifungal antibiotics, dihydrostreptomycin, humidin and cobalamin to inhibit sweet potato black rot pathogenic bacteria and strengthen the disease prevention effect. The microbial fertilizer provided by the invention is safe to human and livestock, and is environment-friendly. Application of the microbial fertilizer provided by the invention to control of sweet potato black rot is not easy to produce drug resistance. The microbial fertilizer has the advantages of simple preparation method, low cost and easy use.