The invention discloses microbial ecological organic fertilizer and a preparation method thereof. The organic chemical fertilizer comprises the following components: edible mushroom dregs, sugarcane dregs, peat soil, oil squeezed waste, filter sludge, livestock and poultry manure and a microbial agent, wherein the microbial agent comprises bacillus subtilis, saccharomycetes, aspergillus niger, guanyloribonuclease, trichoderma, lactobacillus, photosynthetic bacteria, actinomycetes and streptomyces microflavus. The prepared organic fertilizer has advantages of wide raw material source, low cost, high absorption utilization rate, comprehensive nutrients, low dosage, no odor, fast fertilizer effect, various bacteria types, high content, capability of preventing injurious pests, simple preparation method and the like.