The invention discloses an ecological special fertilizer of common yam rhizome. The ecological special fertilizer is prepared from animal waste, coprinus comatus waste materials, cakes, straw, ETS compound bacteria, phanerochaete chrysosporium, JT compound bacteria, mountain soil, amino acid, urea, diammonium phosphate, potassium sulfate, magnesium sulfate, copper sulfate, ferrous sulfate, zinc sulfate, manganese sulfate and dolomite dust. The invention further discloses a preparation and application method of the ecological special fertilizer. The prepared ecological special fertilizer is reasonable in nutritional ingredient ratio, the nutrition requirements of common yam rhizome at all growth stages are met, the number of beneficial bacteria in common yam rhizome planting soil is increased, enzymatic activity in common yam rhizome planting soil is increased, ecological balance of the common yam rhizome plant rhizosphere soil environment is achieved, the soil structure is obviously improved, the stress resistance of common yam rhizome is enhanced, the morbidity and disease index of common yam rhizome are decreased, the aims of high yield and high quality are achieved, and the ecological virtuous circle of common yam rhizome production is achieved.