The invention discloses microorganism organic fertilizer and a preparation method thereof. The microorganism organic fertilizer comprises a microorganism microcapsule and organic fertilizer, wherein amass ratio of the microorganism capsule to the organic fertilizer is (0.08 to 0.11) to 1; the microorganism microcapsule comprises a capsule core and a capsule wrapper, and the mass ratio of the capsule core to the capsule wrapper is 1 to (8 to 10); the capsule core is prepared from microorganism and hydroxypropyl methyl cellulose, wherein a mass ratio of microorganism to hydroxypropyl methyl cellulose is1 to (0.4 to 0.6), the microorganism is prepared from 14 to 16 percent of nitrogen-fixing bacteria, 13 to 15 percent of phosphobacteria, 13 to 15 percent of potassium bacteria, 18 to 20 percent of high temperature bacteria, 18 to 20 percent of actinomycetes, and 18 to 20 percent of cellulose bacteria; and the capsule wrapper is prepared from 60 to 62 percent of polyether-ether-ketone, 10to 12 percent of hydroxypropyl methyl cellulose, 5 to 7 percent of leucine and 21 to 23 percent of epoxy resin binder; and the water content in the organic fertilizer is less than 2 percent by weight,and the quality difference of the product can be reduced.