The invention discloses a production method of a special compound fertilizer for lotus roots. The method comprises the following steps: S1, uniformly mixing livestock and poultry manure and crushed straw according to a mass ratio of 2: 1 to obtain an organic matter mixture; placing microbial strains into a culture medium and comprising saccharomycetes, photosynthetic bacteria, rhizobium and sporebacteria, wherein the content of microorganisms in lotus root growth sludge is supplemented, the decomposition capacity of nutrient substances is improved, absorption of lotus roots is facilitated, and phosphorus-potassium fertilizer, urea, microelements, hexaurea ferric trinitrate and plant ash are mixed into a fermentation product; fully stirring and mixing the raw materials, then adding the radix puerariae powder and the tapioca flour, and fully and uniformly stirring to obtain a viscous mixed material, so that the toughness of the fertilizer can be improved, the loose texture of the fertilizer can be avoided, and slowly decomposing the fertilizer, continuously and efficiently providing nutrients for lotus roots, bysetting the extrusion granulation components, it is possible to push thefertilizer after molding, preparing fertilizer particles with uniform texture and balanced compactness , and realizing high-quality production of the fertilizer.