The invention relates to the technical field of agricultural planting, in particular to compound fertilizer for preventing and treating wheat scab and an application method thereof. The compound fertilizer is prepared from the following raw materials in parts by weight: 5-15 parts of thiram wettable powder, 40-50 parts of straws, 28-35 parts of livestock manure, 14-29 parts of urea, 31-36 parts ofmonopotassium phosphate, 2-5 parts of borax, 2-4 parts of borax, 1-3 parts of magnesium sulfate, 2-6 parts of ferrous sulfate, 9-15 parts of sodium selenite, 40-60 parts of Chinese herbal medicine extract, 0.5-2.5 parts of a fermentation inoculant, 1-2 parts of cellulase and 1-4 parts of brown sugar. The compound fertilizer for preventing and treating wheat scab and the application method thereofare provided by the invention, and various medicaments are perfectly combined together by combining a traditional Chinese medicine medicament with sterilization and parasite expelling effects according to different action mechanisms of the medicaments, so that various wheat diseases such as the wheat scab can be prevented and treated, physical and chemical properties of soil are also improved, fertilizer utilization rate and soil fertility are improved, beneficial microflorae in the soil are enriched, and pollution of harmful substances on the soil is reduced.