The invention relates to a modified diatomite microecological preparation and a preparation method thereof. The microecological preparation is prepared from the following raw materials in parts by weight: 15-25 parts of lactic acid bacteria, 9-14 parts of candida utilis, 9-13 parts of bacillus subtilis, 10-16 parts of enterococcus faecalis, 45-55 parts of diatomite, 9-13 parts of fructo-oligosaccharide, 8-13 parts of aspergillus niger, 5-8 parts of aspergillus oryzae, 5-9 parts of lactobacillus acidophilus, 20-25 parts of bifidobacteria, 5-10 parts of bacillus licheniformis, 0.5-2 parts of bean dregs, 5-10ml of acetic acid, 5-10 parts of FeCl3, and an appropriate amount of water. The lactic acid bacteria, the candida utilis, the bacillus subtilis and the enterococcus faecalis which are screened out are all adapted to grow under meta-acid environment, have strong resistance to animal intestinal mucosa and strong field planting capacity, and are high in reproductive performance; and through optimized arrangement of species, synergistic efficacy is sufficiently exerted, the decomposition of protein, fat and cellulose by metabolism products is strengthened, and the pH value in the animal intestines can be reduced by produced lactic acid and other organic acids, so that growth and propagation of other microorganisms are restrained, and the microecological preparation has a certain bacterial function.