A liquid composite microorganism fertilizer and the preparation method thereof belong to the field of the microorganism fertilizer technique. The invention uses four microorganisms of bacillus subtilis, bacillus magaterium, silicate bacterium and Streptomyces Jingyingensis for mixed-zymolysis and is combined with soluble nitrogen, phosphorus and potassium to prepare the liquid composite microorganism fertilizer. The fertilizer can be used for all type of soil and crops, the application effect on vegetable, fruit is optimum, and the fertilizer has the effects of improving the soil structure, increasing the water-keeping and fertilizer-keeping capability of the soil, and better increasing the production and improving the crop quality.