Fusarium infection of wheat can lead to scab, mycotoxin contamination and yield reduction. Fusarium is a serious threat to food security. In this study, the Fusarium strains in wheat were isolated and identified. The three strains N1, N2 and N3 belonged to Fusarium graminearum, Fusarium asiaticum and Fusarium culmatum, respectively. The production of zearalenone, vomitoxin and fumonisin by the three strains was analyzed by toxin-producing gene detection and mycotoxin detection. The results showed that N1 and N3 could produce zearalenone and vomitoxin, but did not produce fumonisin, while N2 did not produce these three toxins. In this study, ozone and chlorine dioxide were further used for gas fumigation to explore the effect of gas fumigation on the three strains isolated. By observing the spore morphology, mycelium length and mycelium morphology, the results showed that chlorine dioxide fumigation could effectively inhibit the growth of mycelium and spore germination, while ozone could only inhibit spore germination and had no obvious inhibitory effect on the growth of mycelium.