The invention discloses a silkworm excrement and bacillus amyloliquefaciens ZFH-3 containing multifunctional biological fertilizer and an application thereof. The silkworm excrement and bacillus amyloliquefaciens ZFH-3 containing multifunctional biological fertilizer is prepared from raw materials in parts by weight as follows: 25-84.9 parts of silkworm excrement, 10-45 parts of tobacco stems and 0.1-30 parts of a bacillus amyloliquefaciens ZFH-3 microbial agent. The silkworm excrement and bacillus amyloliquefaciens ZFH-3 containing multifunctional biological fertilizer is ecological and safe and can improve the content of organic matters in the soil, loosen the soil, activate the nutrient, increase the use ratio of the soil nutrient, increase soil fertility and beneficial bacteria of the soil, maintain the soil microorganism balance, activate the adversity-resistance system of crops, improve the crop nutrient absorbing ability, reduce and inhibit soil-borne diseases and repel soil insects and nematode, use of chemical fertilizers and pesticide is reduced, and the ecological environment of the soil is improved.