The invention relates to a composite micro-ecological preparation and application thereof, in particular to a composite micro-ecological preparation containing multiple probiotics and application thereof. The preparation contains any three or four of bacillus licheniformis CGMCC No. 2383 powder, bacillus subtilis powder, enterococcus faecalis CGMCC No. 2386 powder, lactobacillus acidophilus powder and saccharomyces cerevisiae CGMCC No. 2388 powder. The preparation has high content of live bacteria, and has the adversity resistance such as gastric acid resistance, bile salt resistance, high-temperature resistance, common antibiotic resistance and the like and the probiotic functions of producing acid and enzyme and resisting pathogenic bacteria. The variety and the proportion of the probiotics and carriers can be determined according to different animals and different animal growth phases. The micro-ecological preparation can improve the feed utilization efficiency, increase the yield of meat, eggs and milk, promote the growth of animals, improve the immunity and the disease resistance of the animals, replace the antibiotic and improve the quality of animal products.