The invention provides a composite bacillus preparation containing three strains, a preparation method of the composite bacillus preparation and application of the composite bacillus preparation to ecological breeding, and belongs to the technical field of microorganism and feed additives. Bacillus coagulans, butyric acid clostridia and bacillus megaterium are used as fermentative strains respectively, and large-scale, low-cost and high-density fermentation production of spores is conducted through step-by-step magnification; three live bacterium preparations are prepared by mixing bacterial sludge with the spores and dry starch; the three live bacterium preparations are matched according to the equal weight ratio, the composite bacillus preparation is obtained, and the concentration of the spores reaches more than 1*108-109 cfu/g; the composite bacillus preparation serves as a microorganism and feed additive to be added to farmed animal feed according to the mass ratio ranging from 0.02% to 0.5%. The composite bacillus preparation is simple and stable in process, low in cost, high in spore content and environment tolerance, easy to store and high in survival rate; the purposes of composition and synergism are achieved through the collaborative supplementary effects of different bacilli in the aspect of micro-ecology adjustment, growth of farmed animals is promoted, the feed utilization rate and feed rewards are increased, diarrhea is prevented and reduced, and the breeding ecological environment is improved.