The invention relates to a biological organic fertilizer adopting microbial fermentation and a preparation method thereof. The method comprises the following steps: firstly uniformly mixing pig manure, chicken manure, cow manure, grass carbon, vegetable cake, sawdust and bran according to weight proportion, then adding biological active water with certain concentration, stirring uniformly, and simultaneously regulating pH to be 6.9-8.9 to start fermentation, overturning every 2-7 days after stacking (when the temperature in the stack can reach 55 DEG C), then stacking in a concentrated way for fermentation again until fermentation maturing is finished (the total time is 7-15 days), namely, the temperature does not rise any more; and drying, smashing, screening and packing the obtained material when the water content is lower than 20 percent, thus obtaining the product. The organic fertilizer not only can improve soil, replace chemical fertilizers, cause yield of crops to be increased and improve crop quality, but also can reduce the content of harmful element, eliminate pesticide residue in soil, and can improve saline-alkali soil.