The invention provides a seed initiator preparation method, which includes adding N-cocoyl compound amino acid, Bacillus subtilis fermentation product, vitamin E, Lanthanum chlorideheptahydrate, salicylic acid and gamma-aminobutyric acid into a blending kettle and mixing to prepare the seed initiator, wherein the Bacillus subtilis fermentation product is prepared by the following process: inoculating a Bacillus subtilis seed liquid into a fermentation medium containing glutamic acid, methylene salicylic acid bacitracin and trichostatin A, culturing, and drying to obtain the Bacillus subtilis fermentation product. The preparation method promotes Bacillus subtilis to metabolize more gamma-polyglutamic acid and new substances, and improves the yield of N-cocoyl compound amino acid; the stability, slow release and shelf life of the seed initiator can be improved, the obtained seed initiator can improve the seed germination ability and the seed germination rate, remarkably improve the tolerance of the obtained rice seedlings to drought stress and high salt stress and the accumulation of lysine, and improve the nutritional value of the obtained rice.