The invention discloses a preparation method of a fertilizer specially used for paddy rice. The preparation method includes the following steps: 1) pyrolyzing bamboo powder at high temperature and adding urea with mixing, adding dipotassium phosphate to the mixture in an inert atmosphere, heating the mixture for activation, and cooling the mixture to room temperature; 2) adding collagen protein, soya bean protein and water to the mixture, heating and stirring the mixture, adding polyvinyl alcohol and potassium persulfate, uniformly mixing the components, regulating the pH value of the mixture to 6.4-6.8 and adjusting temperature, stirring and cooling the mixture, and spray-drying the mixture to prepare a material A; 3) uniformly mixing the material A with diammonium phosphate, potassium chloride, zinc sulfate, borax and nano-bentonite, feeding the mixture to a drum coating machine, increasing the temperature to preheat the mixture, spraying wintergreen oil on the mixture, continuously stirring the mixture, and discharging and air-drying the mixture to prepare a premix B; and 4) feeding the premix B to the drum coating machine, increasing the temperature to preheat the premix B, spraying molten paraffin on the premix B, continuously stirring the premix B, and discharging and drying the premix B to produce the fertilizer specially used for paddy rice.