The invention relates to antibacterial peptide active organic fertilizer and a preparation method thereof and belongs to the technical field of agricultural fertilizer. The fertilizer consists of livestock and poultry excrement, silkworm excrement and a microbial fermenting agent. The preparation method for the fertilizer comprises the following steps: 1) weighing the livestock and poultry excrement, the silkworm excrement and the microbial fermenting agent according to the weight ratio, mixing, adjusting the water content of the mixture to 55 to 65 percent, adjusting the pH value to be 5.0 to 8.0, and adjusting the C / N value to be 20 to 30; 2) performing primary stacked fermentation; 3) performing secondary stacked fermentation; and 4) screening the fermented organic fertilizer obtained in the step 3) to remove impurities, pelleting, shaping, discharging, drying, cooling, removing dust, detecting and packaging to obtain the antibacterial peptide active organic fertilizer. Compared with control, the antibacterial peptide active organic fertilizer can increase the yield by 20.1 to 25.3 percent when applied in the fields of fruits, vegetables, grain and oil, flowers and trees, tea and the like.