The invention belongs to the technical field of grain storage, and discloses a bacillus subtilis strain having broad-spectrum antagonism for main grain storage hazard-moulds, a preparation method of an antifungal metabolite of the bacillus subtilis strain, and application of the bacillus subtilis strain and the antifungal metabolite in grain storage. The strain is bacillus subtilis LM3403, and has a preservation number of CGMCC No. 9377. The bacillus subtilis LM3403 has a better inhibiting effect for the main grain storage hazard-moulds such as fusarium graminearum, fusarium moniliforme, aspergillus flavus, aspergillus niger, aspergillus glaucus, aspergillus fumigatus, penicillium oxalicum, penicillium expansum and mucor mucedo, and is wide in antibacterial spectrum, thus having a giant application potential. The antifungal metabolite of the bacillus subtilis LM3403 has an obvious inhibiting effect for the growth of the main grain storage hazard-moulds. The storage test results prove that after the antifungal metabolite of the bacillus subtilis LM3403 is added into stored grains, the growth of the moulds can be effectively inhibited in a grain storage process, so that the grain storage safety is guaranteed.