The invention provides a biological organic fertilizer prepared by aerobic fermentation of a biogas residue and a preparation method thereof. The preparation method comprises the steps: mixing the biogas residue and a swelling agent to form a fermentation raw material, inoculating a compound microbial agent in the fermentation raw material, uniformly mixing for fermenting, and adding urea, diammonium phosphate, a potassium chloride inorganic salt, brown nitrogen-fixing bacteria, mycorrhiza fungi, silicate bacteria, photosynthetic bacteria acetic bacteria, bifidobacterium, and saccharomycetes after the fermentation is completed to prepare the biological organic fertilizer, wherein the compound microbial agent comprises strains of bacillus, pseudomonas, staphylococcus, streptomyces, penicillium, aspergillus and trichoderma. The compound microbial agent prepared by using the biological organic fertilizer has a pertinence to aerobic fermentation of the biogas residue, and is capable of effectively increasing the fermentation rate of the biogas residue, shortening the fermentation time and realizing high-additional value production, innocent treatment and recycling of the biogas residue; and the problem of resources and environment of villages and small towns is solved, and the rapid development of construction of new countryside and towns and cities can be promoted.