In response to the urgent need for performance predictions of damaged aerospace structures, this study undertakes a comprehensive investigation into the flutter characteristics of damaged variable-stiffness composite laminate (VSCL) plates. The governing boundary value problem for the dynamics of damaged VSCL plates is formulated using first-order shear deformation theory (FSDT). Additionally, the first-order piston theory is utilized to model the aerodynamic pressure in supersonic airflow. A novel coupling methodology is developed through the integration of penalty function methods and irregular mapping techniques, which effectively establishes the interaction between damaged and undamaged plate elements. The vibration characteristics and aeroelastic responses are systematically analyzed using the Chebyshev differential quadrature method (CDQM). The validity of the proposed model is thoroughly demonstrated through comparative analyses with the existing literature and finite element simulations, confirming its computational accuracy and broad applicability. A notable characteristic of this research is its ability to accommodate arbitrary geometric configurations within damaged regions. The numerical results unequivocally demonstrate that accurately predicting the flutter characteristics of damaged VSCL plates constitutes an effective strategy for mitigating structural stability degradation. This approach provides valuable insights for aerospace structural design and maintenance.