The effects of mineral nutrient on banana wilt disease, which are the result of a competitive relationship between host plants and pathogens, can affect the interactions of plants with microorganisms. To investigate the mineral nutrient effect, hydroponic experiments were conducted in glasshouse containing combinations of low, medium, and high iron (Fe) and boron (B) concentrations, followed by pathogen inoculation. High Fe and B treatment significantly reduced the disease index and facilitated plants growth. With increasing Fe and B concentrations, more Fe and B accumulated in plants. High Fe and B treatment dramatically reduced the Fusarium oxysporum conidial germination rate and fungal growth compared with the other two treatments, contributing to decreased numbers of the pathogen on infected plants. Furthermore, High Fe and B treatment decreased the fusaric acid production of F. oxysporum in vitro and also increased the mannitol content of the plants, which in turn decreased the phytotoxin production of infected plants and finally reduced the disease index due to the virulence factor of phytotoxin. Taken together, these results indicate that Fe and B play a multifunctional role in reducing the severity of diseases by affecting the growth of F. oxysporum and the responses between plants and pathogens.