The invention discloses a composite microecological preparation and an application thereof. The composite microecological preparation comprises saccharomycetes, acid-producing bacteria and bacillus, wherein the viable count ratio of the saccharomycetes to the acid-producing bacteria to the bacillus is (1-3): (1-4): (1-2), the effective viable count of each gram of the composite microecological preparation is greater than or equal to 1010 CFU/g, the saccharomycetes are selected from at least one of saccharomyces cerevisiae, phaffia rhodozyma, rhodotorula mucilaginosa and candida utilis, the acid-producing bacteria are selected from at least one of lactobacillus plantarum, enterococcus faecalis, enterococcus faecium, clostridium butyricum and lactobacillus rhamnosus, and the bacillus is selected from at least one of bacillus subtilis, bacillus licheniformis, bacillus coagulans, bacillus amyloliquefaciens and bacillus megatherium. According to the composite microecological preparation and the application thereof, the intestinal health level of animals can be improved, the growth of the animals can be promoted, the anti-stress capability of the animals can be improved, the immune system of the animals can be activated, and diseases can be reduced.