Potato (Solanum tuberosum L.) is ranked as the fourth largest staple crop in China. However, potato production is increasingly threatened by Verticillium wilt (VW) caused by the fungus Verticillium dahliae in various provinces. In the present study, we explored the application of star polycation (SPc) nanocarrier to improve the effectiveness of the fungicide fluxapyroxad (Flu) in combating VW. The SPc self-assembled with Flu through hydrogen bonds and van der Waals forces to form the Flu/SPc complex spontaneously, which exhibited strong intermolecular interactions, as indicated by a high affinity constant and favorable thermodynamic parameters. Complexation with SPc decreased the particle size of Flu. The Flu/SPc complex had a greater effect on V. dahliae than Flu alone, reducing the colony diameter and spore numbers more effectively. Expression levels of multiple key genes involved in nitrogen, polysaccharide, and sugar metabolism were downregulated in V. dahliae upon Flu/SPc complex treatment compared to Flu treatment, which might contribute to the greater growth inhibition in Flu/SPc-treated samples. Uptake studies in potato plants demonstrated that SPc significantly enhanced the absorption of Flu compared with Flu alone. Slighter disease symptoms and lower fungal biomass in greenhouse and field trials confirmed the enhanced protective effects of the Flu/SPc complex on potato seedlings. This is the first report that a self-assembled nanofungicide limits V. dahliae growth and protects potatoes from destructive VW.