The invention provides a microbial organic fertilizer and a preparation method thereof. The preparation method comprises the steps of strain culture, compounding and liquid submerged fermentation, and belongs to an agricultural integrated production technique. 15-20% of Bacillus mucilaginosus, 15-18% of Bacillus megaterium, 15-18% of Azotobacter chroococcum, 10-13% of Saccharomyces cerevisiae, 10-13% of Candida utilis, 15-18% of Lactobacillus plantarum and 10-13% of actinomycete are respectively subjected to primary and secondary strain culture and tertiary liquid submerged fermentation until the bacterial count in the fermentation liquid reaches 10-15*10<8>/mL, thereby obtaining the microbial organic fertilizer (707(Y)). By adopting the advanced liquid submerged fermentation technique and using the strains with high stability and functionality, which are screened from the natural world over the years and have the advantages of many varieties and convenient application method, the invention can promote the plant growth, improve the fruit quality, promote prematurity, increase the yield, enhance the utilization ratio of the fertilizer, improve the ecological environment of soil, and have certain effects of disease prevention and disease resistance.