The invention discloses a special complex microbial agent for harmless treatment of livestock and poultry excrements. The special complex microbial agent is prepared from the following raw materials in parts by weight: 0.02-0.04 part of bacillus mucilaginosus, 0.01-0.03 part of bacillus licheniformis, 0.01-0.03 part of streptomyces jingyangensis whey powder, 0.01-0.02 part of azotobacter vinelandii, 0.04-0.08 part of aspergillus spore powder, 0.01-0.03 part of streptococcus thermophilus, 0.01-0.02 part of enterococcus faecalis, 0.02-0.04 part of antimicrobial peptide thallus, 80.0-120.0 parts of dried silkworm dropping, 2.0-6.0 parts of peanut cakes, 2.0-3.0 parts of bran, 7.0-8.0 parts of starch, 3.0-3.5 parts of molasses, 2.0-3.0 parts of monocalcium phosphate, and 1.0-1.4 parts of urea. Used for harmless treatment of livestock and poultry excrements, the special complex microbial agent has the advantages that the fermentation time is short, the quality of a fertilizer is high, the active rate of microorganisms in soil can be activated, the temperature permeability of air in soil can be increased, and the special complex microbial agent has an effect of preventing and controlling various fungal diseases and bacterial diseases, as well as effects of increasing the yield and improving the quality while providing complete nutrients for the crop, thus having better economic benefits, social benefits and ecological benefits.