The invention relates to an inorganic-organic microbial compound fertilizer and a preparation method thereof. The inorganic-organic microbial compound fertilizer is characterized by comprising ordinary high-concentration three-element compound fertilizer, humic acid, fly ash, microbial compound bacteria powder and other elements, wherein the microbial compound bacterial powder is obtained by mixing bacterial powders which are prepared by respectively fermenting and culturing photosynthetic bacteria, yeast, lactic acid bacteria, bifidobacterium, bacillus subtilis, bacillus licheniformis, bacilluslaterosporus, bacillus megaterium, bacillus mucilaginosus, azotbacteria chroococum and actinomycetes. In the inorganic-organic microbial compound fertilizer, the microbial content of the yeast is no less than 2.0*108cfu/g, and the microbial contents of the other strains are all no less than 2.0*109cfu/g. The inorganic-organic microbial compound fertilizer can centralize the advantages of an organic fertilizer, an inorganic fertilizer and microorganisms, thereby enhancing the stress resistance and the disease resistance of crops, enhancing the fertilizer absorption ability of the crops, lowering the soil hardening degree and improving the soil ecological environment and the quality of the crops.