The invention discloses a special controlled-release fertilizer for lotus roots and a preparation method thereof. The preparation method comprises the following steps of preparing a fertilizer core by urea, potassium chloride, calcium phosphate, a trace element fertilizer, an inhibitor and a dispersant; performing inner coating treatment on the fertilizer core by an inner coating film agent which is prepared from polylactic acid, polyethylene glycol and ethyl alcohol; performing outer coating treatment on the fertilizer core by an outer coating film agent which is prepared from polyacrylate, ethylene propylene diene monomer, modified starch, acetone and water, so as to obtain the special controlled-release fertilizer for the lotus roots. Compared with the prior art, the special controlled-release fertilizer has the advantages that the nutrient elements in the fertilizer are rich, the utilization rate of a nitrogen fertilizer is high, the controlled-release property is good, and the nutrient requirement of the lotus root in each growth period is met; the outer coating can be recycled, so that the environment-friendly effect is realized; the inner coating can be completely degraded, so that the danger to surrounding environment is avoided.