Corn ear rot has been the most important disease of the world. It is mainly caused by Fusarium moniliforme which produce a number of mycotoxins including Fumonisin B1 (FB1). Aiming at supplying a potentially effective biological control agent against F. moniliforme, Bacillus megaterium MHT6 isolated from China, was tested for its antagonistic activity against F. moniliforme. Moreover, both antifungal activity and the active compound of strain MHT6 were tested and identified. In order to improve its antifungal activity, a random mutagenesis generated using He-Ne laser irradiation was applied on B. megaterium MHT6. After the mutation, one hundred bacterial colonies were obtained and their effects against F. moniliforme were assessed in a plate assay. Eight colonies (8%) exhibited higher inhibition activity as compared to the wild type MHT6. Among them, the mutant MHT 88 which showed the strongest antagonistic ability was selected out. Through bacterial motility assays, the mutant MHT88 showed stronger swarming motility than wild type MHT6. According to FPLC and MALDI-TOF-MS, the production of two main antagonistic lipopeptides such as surfactin and fengycin increased in mutant MHT88. Especially the surfactin, which can't be detected in the wild strain MHT6, was obviously observed in mutant. Moreover, the cell-free supernatant of the mutant MHT88 showed stronger capability in degrading FB1 compared to MHT6. This study provided a promising biological agent to inhibit F. moniliforme and suppress corn ear rot disease.