This study employs computational fluid dynamics (CFD) to investigate the aerodynamic performance and static stability of hybrid wing aircraft, considering the interference of counter-rotating embedded propellers. Extensive numerical verification has been carried out, including comparisons with NASA’s high-lift propeller (HLP) data. Three configurations—no propeller, counter-rotating inboard-upwash (CNIU) and counter-rotating outboard-upwash (CNOU) are defined to analyze the aerodynamic force/moment characteristics and flow field structures over a range of angles of attack from −6° to 26°, in conjunction with crosswind velocities of 0, 5, 10, and 15 m/s. The propeller-induced slipstream alters the aircraft’s fundamental performance by modifying wing pressure distributions and vortex systems. Specifically, the CNIU configuration increases the low-pressure areas on both the fuselage and outer wing upper surfaces, enhancing the lift-to-drag ratio by 28.4% at low angles of attack. In contrast, the CNOU configuration improves longitudinal steady-static margin by 27.4% under typical conditions and demonstrates superior lateral static stability under 10 m/s leftward crosswind conditions. For engineering applications in the aerodynamic design of such aircraft, the CNIU configuration is recommended for high cruise efficiency, whereas the CNOU configuration is preferred for flight stability.