Using soybean lecithin as an emulsifier and rapeseed oil as the oil phase, a stable nanoemulsion system encapsulating yakuchinone B was prepared. The preparation conditions for the nanoemulsion were optimized through single-factor experiments and response surface methodology. Measurement of the emulsion was performed using a nanoparticle size analyzer, a laser confocal microscope, and a Fourier transform infrared spectrometer to assess the particle size, polydispersity index(PDI), Zeta potential, encapsulation efficiency, stability, and spectral characteristics. The results indicated that under the optimal preparation process parameters(soybean lecithin mass concentration of 18.4 g/L, homogenization pressure of 172.35 MPa, homogenization cycles of 7, and yakuchinone B mass concentration of 7 mg/mL), the average particle size of the yakuchinone B nanoemulsion was (175.37±4.33) nm, the PDI was 0.13±0.02, and the encapsulation efficiency was (91.00±0.03)%. The encapsulation amount of yakuchinone B did not affect the particle size and PDI of the emulsion, and the nanoemulsion with 7 mg/mL of yakuchinone B had the highest encapsulation efficiency. The microstructure of the yakuchinone B nanoemulsion was spherical and uniformly distributed. When stored at 4 °C for 28 days, there were no significant changes in the particle size, PDI, and encapsulation efficiency of the emulsion, demonstrating the system’s stability. When the concentration of added NaCl was ≤30 mmol/L, the emulsion could maintain a relatively stable state. When the NaCl concentration was ≥50 mmol/L, the particle size and PDI of the emulsion increased significantly, and the absolute value of the Zeta potential decreased significantly, leading to a decrease in emulsion stability. There were no covalent bonds formed between rapeseed oil, soybean lecithin, and huperzine B, and no chemical interactions occurred.