To improve the bioavailability of the poorly water-soluble fungicide, an azoxystrobin nanosuspension was prepared by the wet media milling method. Due to their reduced mean particle size and polydispersity index, 1-Dodecanesulfonic acid sodium salt and polyvinylpyrrolidone K30 were selected from six conventional surfactants, the content only accounting for 15% of the active compound. The mean particle size, polydispersity index, and potential of the nanosuspension were determined to be 238.1 ± 1.5 nm, 0.17 ± 0.02 and − 31.8 ± 0.3 mV, respectively. The lyophilized nanosuspension mainly retained crystalline state, with only a little amorphous content as determined by powder X-ray diffraction. Compared to conventional fungicide formulations, the nanosuspension presented an increased retention volume and a reduced contact angle, indicating enhanced wettability and adhesion. In addition, the azoxystrobin nanosuspension showed the highest antifungal activity, with a medial lethal concentration of 1.4243 μg/mL against Fusarium oxysporum. In optical micrographs, hyphal deformations of thinner and intertwined hyphae were detected in the exposed group. Compared to the control group, the total soluble protein content, superoxide dismutase, and catalase activities were initially increased and then decreased with prolonged exposure time. The azoxystrobin nanosuspension reduced the defensive antioxidant capability of Fusarium oxysporum and resulted in the generation of excessive reactive oxygen species. This study provides a novel method for preparing nanosuspension formulation of poorly soluble antifungal agents to enhance the biological activity and decrease the negative environmental impact.