The invention discloses an organic medicinal fertilizer with antibacterial and anthelmintic activities and a preparation method thereof. The active organic fertilizer contains 10-20 parts of Aconitum, 5-10 parts of Liwu, 4-8 parts of Artemisia chinensis, 10-15 parts of chamaejasma, 20-30 parts of Oxytropis, 2-3 parts of Drunken Horse Grass, and 5- 10 parts, 3-8 parts of Artemisia chrysanthemum stems, leaves, seeds, 50-60 parts of mushroom dregs, 10-20 parts of cottonseed meal, 5-10 parts of rice husks, crush the raw materials to replenish water, and after solid material microwave technology treatment, add According to 80g / T to 120g / T of active biological complex bacteria for composting and fermentation, the active biological complex bacteria are prepared by directly mixing Bacillus jelly-like, Bacillus megaterium, Bacillus subtilis, Glomus moses and Glomus terrestriale Antibacterial active biological organic fertilizer. The organic medicinal fertilizer provided by the invention contains antibacterial and anthelmintic components and an organic medicinal fertilizer with active organisms, and has wide application value.