Bacillus subtilis JA antagonized the growth of Gibberella zeae. In order to reduce growth of this fungi pathogen to a greater extent, low-energy ion beam implantation was applied in mutant breeding. We studied the effects of different energies and different doses of nitrogen ion implantation. The mutant strain designated as JA026 was obtained showing higher inhibition activity in the screening plate. Its inhibition zone against indicator organism increased by 14.3% compared to the original strain. The electrospray ionization mass spectrometry (ESI/MS) analysis indicated that the antifungal lipopeptides produced by the mutant were identical to those produced by the wildtype strain. The mutant strain exhibited favorable properties including the high yield of antifungal lipopeptides production and faster growth over the parent strain, which suggested that this strain would be a promising biocontrol candidate in agriculture.