The invention discloses a rice-duck symbiotic compound microbial fertilizer, which is mainly prepared from urea, potassium phosphite, ammonium sulfate, potassium chloride, plant meal, potassium fulvate, calcium magnesium phosphate fertilizer, pyroligneous liquor, a decomposing inoculant, colletotrichum gloeosporioides, bacillus amyloliquefaciens, an insect expelling component, active nano siliconand duckweed seeds. The preparation method comprises the following steps: mixing the plant meal and the decomposing inoculant, carrying out compost fermentation, spraying the pyroligneous liquor on the surface of the compost to obtain an organic fermentation material, crushing the organic fermentation material, and mixing the crushed organic fermentation material with other raw materials to obtainthe rice-duck symbiotic compound microbial fertilizer. According to the invention, the nano active silicon is introduced into the rice-duck symbiotic compound microbial fertilizer, the particle sizeof the nano active silicon is nanoscale, the nano active silicon is easily absorbed by crops, and the nano active silicon can activate plant cells, promote metabolism of organisms, improve immunity ofthe organisms, enhance growth vigor of the plants and improve disease resistance, stress resistance and lodging resistance of rice, and prevents ducks from damaging the rice.