The invention relates to a microbial fertilizer and a preparation method thereof. The preparation method is as follows: bacillus cereus, bacillus megaterium and bacillus subtillis are mixed and fermented; bacillus mucilaginosus, pantoea agglomerans and azotobacter chroococcum are fermented respectively; the four fermented cultures are mixed and filled according to a certain proportion so as to produce a microbial blend which is used by the methods of seed soaking, root irrigation and spraying. The microbial fertilizer can promote plant rhizosphere growth and propagation, improve soil, eliminate soil hardening, enhance soil permeability and promote the development of the root system; the microbial fertilizer has the advantages of releasing potassium and phosphorus, fixing nitrogen, improving fertilizer efficiency and reducing the amount of chemical fertilizer used, inhibiting the propagation of harmful bacteria in the soil, preventing the diseases such as soil-borne diseases, replant disease and the like; thus realizing the functions of increasing income and improving the quality of agricultural products.