This study presents a performance-driven control strategy incorporating a super-twisting algorithm, which enforces the tracking error of a multi-body folding wings system to evolve within the bounds prescribed by a performance function, effectively addressing the challenges arising from aerodynamic load variations, gravity-vector reversals, and external disturbances during coordinated morphing maneuvers. A dynamic model of the folding-wing system incorporating unsteady aerodynamic effects is first established. Then, leveraging positive system theory and Metzler matrix properties, the proposed control framework ensures that the deviation between the tracking error and the prescribed performance boundaries remains non-negative, thereby guaranteeing strict error confinement. The introduction of the Super-Twisting Algorithm as a robust compensation enables the continuous cumulative estimation and cancellation of disturbances, while significantly suppressing high-frequency switching in the control torque, thereby achieving smooth control inputs. Simulation results confirm that the proposed method maintains smooth control responses and bounded tracking errors even under structural deformation and time-varying aerodynamic disturbances, demonstrating its robustness and practical applicability.