The invention relates to bacillus megaterium, a polypeptide agricultural microbial agent thereof as well as a preparation method thereof and applicationof the polypeptide agricultural microbial agent.The bacillus megaterium takes distillers' grains, soya bean meal and straw powder, which are rich in protein content, as main raw materials, and are mixed with corn flour, wheat bran, inorganic saltsand a few carbon source to reasonably compound and steam; high-yield protease bacillus subtilis is firstly utilized, the bacillus megaterium is utilized for decomposing different proteins in raw materials under a special fermentation condition to prepare the agricultural microbial agent which takes active peptides, amino acid, polysaccharides and the like as efficient ingredients; the microbial agent contains a great number of living spores, 17 free amino acids, a plurality of active peptides, and polysaccharides, and nutrient content is rich, the activity of thallus is high, and shelf life reaches two years or more; and according to the field experiment, the good effects of improving quality and increasing the yield are achieved.