Fungal diseases affecting maize not only reduced maize yields but also generate fungal toxins that pose risks to both human and animal health, particularly when the straw is returned to the field. Microbial in-situ control is considered an environmentally friendly method that effectively addresses the limitations of unstable effects. In this study, we isolated Bacillus velezensis zm026 from rhizosphere soil for in-situ restoration, based on the soil community structure, which exhibits high antagonistic activity against Fusarium verticillioides and Exserohilum turcicum. Zm026 effectively colonized the surface of maize roots within five days and activated the plant immune system, significantly increasing the expression of defense genes such as ZmGST, ZmZHD, ZmPR-1, ZmPR-2, and ZmPR-3. The efficient anti-fungal substance of zm026 was identified by HPLC-MS and determined to be bacillomycin D. Further observations using trypan blue staining, along with DAPI (4',6-diamidino-2-phenylindole) and PI (Propidium iodide) fluorescent staining, revealed that bacillomycin D could inhibit fungal spore germination, disrupt the integrity of fungal cell membranes, induce apoptosis, and cause spore tips to protrude, swell, or rupture. Ultimately, indoor pot experiments demonstrated that the application of zm026 fermentation broth significantly promoted growth, inhibited the onset of fungal diseases in corn, and effectively reduced the abundance of Fusarium spp. in corn grains. This research provides a beneficial in-situ restoration strain for the high-quality development of corn.