The invention mainly relates to the technical field of aquatic products and discloses a special fertilizer applied to lotus roots in an early stage of forming lotus seedpods. The fertilizer is prepared from the following raw materials: corncobs, sawdust, pig manure, chicken manure, sweet potato vines, bagasse, edible fungus culture media, biogas residue, distilled grains, vinegar residue, EM bacteria, active carbon, disease-resistant powder and inorganic fertilizers. The fertilizer is rich in raw materials, balanced in nutrition and rich in organic and inorganic nutrition elements, is capableof accelerating expansion of lotus seedpods and lotus seeds of the lotus roots, enabling the yield of lotus seeds to reach 365kg per mu, enabling the yield of the lotus roots to reach 2694kg per mu, and obviously improving the planting efficiency of the lotus roots; all the other raw materials except the active carbon, the disease-resistant powder and the inorganic fertilizers are firstly crushedand are subsequently fermented for a first time, so that the bacteria proliferation is accelerated and the release of nutrition components in the raw materials is accelerated, and the nutrition absorption of the lotus roots is accelerated; after the active carbon and the disease-resistant powder are added, the raw materials are continuously fermented at low temperature, so that the active carbon fully absorbs the nutrition components and the disease-resistant components; the nutrition components and the disease-resistant components are slowly released in the later stage; the utilization rate of the fertilizer is increased; the occurrence of pests and diseases is reduced; the growth of the lotus seedpods is promoted; the yield of the lotus seeds is improved.