An antifungal lipopeptide iturin A with strong activity against Fusarium oxysporum was produced by honey isolated strain Bacillus amyloliquefaciens BH072. For large-scale biocontrol application, the antifungal effect was deeply demonstrated by structure and mode of action. Cyclic structure and second structure were determined based on situ acid hydrolysis and Fourier Transformed-Infra Red (FT-IR) Spectra analysis. Structure of α-helix was predicted which might be associated with activity. Afterwards, antifungal mechanism of iturin A on F. oxysporum were investigated from fungal cell wall to the plasma membrane and finally to intracellular proteins by morphological, activity of alkaline phosphatase (AKP), conductivity, Malondialdehyde (MDA) and SDS-PAGE detection. Antifungal damage appears on not only the spore germination and mycelium growth of F. oxysporum, but also the leakage of cellular proteins. Moreover, growth of F. oxysporum could be inhibited in the presence of iturin A at a MIC of 2.5 mg/mL. Considered with its high production in previous work, B. amyloliquefaciens strain BH072 and iturin A might be a promising candidate for biocontrol.