Abstract: Bakanae disease is an important seed-borne disease in rice production. However, excessive reliance on chemical fungicides such as prochloraz has led to pronounced resistance problems; therefore, developing biocontrol strategies is of great significance for reducing reliance on prochloraz and enabling its partial replacement. This study prepared a 10% soybean peptide nanoemulsion using a shear emulsification method. Its physicochemical properties were characterized by determining the emulsion type, particle size, Zeta potential, preparation stability, contact angle, and static surface tension. Its antifungal activity against Fusarium fujikuroi and pot efficacy against rice bakanae were evaluated, and the underlying control mechanism was preliminarily explored using transcriptomic analysis. The results showed that the prepared 10% soybean peptide nanoemulsion was a water-in-oil emulsion with an average particle size of 179.8 nm, a D₉₀ of 223.9 nm, and a Zeta potential of + 15.7 mV. The backscattering light intensity varied within a range of − 3.1% to + 1.4%. After storage at 40 ℃ for 56 days, the decomposition rate of soybean peptides in the sample was 1.27%, indicating good stability; The 100 times diluted formulation contact angles on the surface of a polytetrafluoroethylene plate, rice leaves and seeds were 50.1°, 43.5° and 17.9°, respectively. And a static surface tension of 32.06 mN/m, demonstrating favorable wetting and spreading performance. After 48 h of treatment with the diluted formulation, the spore germination rate of F. fujikuroi was only 7.3%, which was significantly lower than that of the sterile-water control (61.3%). Five weeks after inoculation with F. fujikuroi, seed-soaking with the soybean peptide 10% nanoemulsion achieved a pot control efficacy of 62.0% against rice bakanae, which increased to 80.6% when combined with a reduced dose of 25% prochloraz emulsifiable concentrate. Transcriptomic analysis preliminarily elucidated that the nanoemulsion may enhance rice disease resistance by modulating pathways such as plant hormone signal transduction and secondary metabolite biosynthesis. This study can provide a new approach for green management of bakanae disease and other Fusarium crop diseases, while reducing chemical pesticide use and improving control efficacy.