Abstract: The transonic aerodynamic nonlinearities induced by phenomena such as shock wave motion and flow separation can cause significant changes in the flutter characteristics of a morphing aircraft as its configuration evolves. It is a substantial challenge for the lightweight structural design of morphing aircraft. This paper proposes a data-driven transonic aeroelastic modeling method for the wing with variable camber trailing edge, which efficiently and accurately predicts the flutter boundary during the discrete variation of trailing-edge camber. Initially, a numerical simulation method based on computational fluid dynamics (CFD) is developed to capture the unsteady transonic aerodynamic behavior of a wing featuring a variable camber trailing edge. The simulation involves generating snapshot data of the pressure distribution and aerodynamic response on the wing surface under a given excitation signal. These data are then collected and utilized for further analysis. Subsequently, a reduced-order state-space model is constructed using the training data, which is based on the combination of proper orthogonal decomposition (POD) and dynamic mode decomposition with control (DMDc). This model effectively characterizes the complex relationship between the wing’s motion and the distribution of aerodynamic loads, allowing for a more efficient analysis of aeroelastic behavior. Finally, the established reduced-order aerodynamic model is employed to predict the transonic aerodynamic responses, as well as the flutter characteristics of the morphing wing with a variable camber trailing edge. The results from the numerical simulations demonstrate that the proposed data-driven modeling method can reliably forecast the unsteady aerodynamic forces, the surface pressure distribution, and the flutter boundary of the variable camber wing throughout the trailing-edge camber discrete variation process under transonic flow conditions. Additionally, the findings indicate that an increase in the camber angle of the trailing edge leads to the earlier occurrence of the transonic flutter dip.