The present invention relates to a preparation method of a microecology fermented feed by utilizing byproducts of corn deep-processing as raw materials. The preparation method includes: 1, selecting three probiotics of bacillus subtilis, aspergillus oryzae and rhizopus, obtaining a second stage seed by slant culture, first stage seed culture in a shake flask and second stage culture in a shake flask, and carrying out complex formulation according to a certain proportion; 2, selecting three probiotics of lactic acid bacteria, candida utilis and flavor yeast, obtaining a second stage seed by slant culture, first stage seed culture in a shake flask and second stage culture in a shake flask, and carrying out complex formulation according to a certain proportion; 3, reasonably proportioning to prepare a fermentation medium by utilizing the by-products of the corn deep-processing, such as corn bran, embryo cake, corn steep liquor and gluten meal, as raw materials; 4, inoculating the formulated probiotics of the step 1 in a solid state fermentation medium to perform aerobic fermentation, inoculating the formulated probiotics of the step 2 to perform anaerobic fermentation after aerobic fermentation for a while, drying after the fermentation, to obtain the microecological feed. The preparation method has high comprehensive utilization efficiency. The microecological feed has high active proteins, lactic acid and functional small peptides, and is a high quality health care feed which is easily absorbed by body.