The invention relates to a biological organic fertilizer produced by performing microbial fermentation on lignite, vinegar residues, sawdust (straw), shale and the like and a preparation method thereof. The biological organic fertilizer comprises the following components in percentage by mass: 5 to 10 percent of lignite, 50 to 65 percent of vinegar residues, 20 to 25 percent of sawdust (straw), 8 to 10 percent of shale, 1 to 2 percent of magnesium sulfate, 0.5 to 1 percent of zinc sulfate, 0.5 to 1 percent of borax and 0.1 to 0.2 percent of microbial strain. The method comprises the following steps of: selection of microorganisms, activation, first-level amplification, second-level amplification, third-level amplification, mixing, fermentation, turning, obtaining of finished products, low-temperature drying, detection, metering and packaging. After the biological organic fertilizer is applied to protected land, organic matters and humus contained in the biological organic fertilizer can adsorb and fix cations in a free state in soil, the concentration of soil solution and the harm of salinization are reduced, the vegetable growth (harvest) period is prolonged by 10 days, yield is increased by 8.5 to 22.6 percent, morbidity is reduced by 30.3 to 56.3 percent, and the content of nitrate is reduced by 20.5 to 27.8 percent.