This work investigates the effect of wake interference on the nonlinear coupled dynamics and aerodynamic performance of flexible membrane wings at a moderate Reynolds number. A high-fidelity computational aeroelastic framework is employed to simulate the flow-induced vibration of flexible membrane wings in response to unsteady vortex wake flows produced by an upstream stationary circular cylinder. The coupled dynamics of the downstream membrane are investigated at different gap ratios, aeroelastic numbers, and offset distances. The variations in flow features, membrane responses, and frequency characteristics are analyzed to understand the wake interference effect on membrane aeroelasticity. The results indicate that the aerodynamic performance and flight stability of the downstream membrane are degraded under the wake interference effect. Four distinct flow regimes are classified for the cylinder–membrane configuration, namely (i) single body flow, (ii) co-shedding I, (iii) co-shedding II, and (iv) detached vortex-dominated vibration, respectively. The mode transition is found to build new frequency synchronization between the flexible membrane and its own surrounding flows, or the wake flows of the cylinder, to adjust the aerodynamic performance and membrane vibration. This study sheds new light on membrane aeroelasticity in response to wake flows and enhances understanding of the fluid–membrane coupling mechanism. These findings can facilitate the development of next-generation bio-inspired drones that have high flight efficiency and robust flight stability in gusty flows.