The invention discloses a method for producing a complex micro-ecological preparation with microbial agents and enzyme. According to the action principles and characteristics of every microbial strain, the method adopts scientific combination and adds enzyme preparations and acidifier to enable microorganisms in the product to grow rapidly and take dominance in fermented feed and animal bodies so as to reduce the growth opportunity of miscellaneous bacteria. The preparation comprises the following components: bacillus subtilis, lactobacillus plantarum, candida utilis yeast, lactobacillus acidophilus, protease, amylase, cellulase, xylanase, mannanase, galactosidase, pectinase and citric acid. As all strains of the product adopt liquid deep fermentation culture, the non-polluting property of the product is guaranteed. Liquid microbial agents ensure that the number of bacterial colonies of the product is more than 100 million and the product is free from the pollution of other miscellaneous bacteria, while solid microbial agents ensure that the number of bacterial colonies of the product is more than 1 billion and the proportion of miscellaneous bacteria to effective bacteria is not more than 0.0001. The preparation contains bacillus, lactic acid bacteria and yeast, can apply to the processes of making green-yellow storage feed, fermenting feed, soaking feed, and the like, can be directly added to feed for feeding, and can improve the growth performance of ruminant animals, poultry, pigs, aquatic products and special animals.