The invention relates to a special compound fertilizer for chenopodium quinoa willd and a preparation method thereof, belonging to the technical field of crop fertilizer. The special compound fertilizer for chenopodium quinoa willd consists of an inorganic component and an organic component, wherein the mass content of the inorganic component is 30-35%; the inorganic component consists of urea, monopotassium phosphate and calcium superphosphate in a mass ratio of 10:8.2:10; the organic component is prepared by taking agricultural waste, wheat straw, distillers' grains and gypsum as fermentation base materials and performing aerobic fermentation using zymophyte; and the zymophyte consists of aspergillus carbonarius, aspergillus flavus, aspergillus fumigatus, rhizopus oryzae, aspergillus subolivaceus and verticillium lecanii. In the special compound fertilizer for chenopodium quinoa willd provided by the invention, the viable count exceeds 46,000,000(cfu)/g, the organic content exceeds 29.8wt%, and the pH is 6.9-7.1; abundant N, P, K and Ca and various beneficial trace elements are contained; and the yield and quality of chenopodium quinoa willd can be remarkably improved, and the insect damage and disease damage are effectively reduced.