Compound-wing unmanned aerial vehicles (UAVs) are highly valued for their performance. However, during the transition from vertical take-off to the cruise phase, the rotor wake can be coupled with the fixed wing. In this study, the aerodynamic effects of a DJI 9450 rotor on a NACA2415 fixed wing during transition were investigated using the computational fluid dynamics (CFD) method. The rotor-to-wing distances (R/L = 0.25, 0.5, and 0.9) were varied to analyze their impact on aerodynamic performance. The results show that increasing the distance between the front rotor and the fixed wing enhances the lift and drag of the fixed wing, while increasing the distance between the rear rotor and the fixed wing decreases the lift and drag of the fixed wing. During the rotor’s rotation, the fluctuation in the lift and drag of the fixed wing changes periodically due to the rotor wake, and the smaller the distance between the rotor and the fixed wing, the larger the fluctuation. When R/L = 0.25, the fluctuation of the fixed wing is minimized. Compound-wing UAVs with rotors mounted at R/L = 0.25 during the design stage can improve the flight stability during the transition phase in UAVs.