The presence of bleed in an aero engine’s compressor can significantly impact its flow characteristics and contribute to rotating instability. This study focuses on the impact of a typical cavity bleed structure on the internal flow characteristics of a compressor, specifically its circumferential non-uniformity and aerodynamic stability. A numerical simulation involving multiple flow passages was conducted on the transonic high-pressure rotor of the E3 compressor, considering its typical bleed structure. The study delves deep into the non-uniform flow characteristics and the mechanisms behind their generation in the compressor flow field. Furthermore, the influence of bleed on the rotating instability of the compressor is explored by comparing changes in compressor instability and adiabatic efficiency under uniform and non-uniform flow field conditions. The findings indicate that the axial position of the cavity bleed structure plays a crucial role in influencing key parameters such as rotor stall margin, peak efficiency, and total pressure ratio under near-stall conditions. The circumferential non-uniformity, resulting from the presence of the cavity bleed, intensifies with higher bleed air flow rates. For the upstream bleed configuration applied to the rotor, with a total bleed rate of 5%, the maximum variation in absolute flow angle at the inlet of different rotor channels can reach up to 1°. Additionally, the maximum difference in inlet flow coefficient can reach 0.0392. These findings demonstrate that the non-uniformity caused by the typical bleed structure leads to a loss in stall margin for the rotor when compared to a uniform flow field scheme.