Abstract In the realm of aerospace engineering, the analysis of flutter under supersonic flight conditions is of paramount importance. Hybrid nanocomposite materials, known for their lightweight and high-strength properties, are increasingly being employed in aerospace engineering. This article examines the supersonic flutter behavior and reliability of smart hybrid nanocomposite trapezoidal plates, considering various practical factors. The structure is subjected to yawed flow conditions, a scenario often encountered during supersonic flight. The importance of the hybrid nanocomposite in various applications such as aerospace, public security tools, and so on, therefore the hybrid nanocomposite core layer reinforced by carbon nanotubes (CNTs) and carbon fibers incorporates real-world material complexities such as agglomeration, waviness, and random orientation of fibers into the analysis. The complexities and the accurate characterization of the hybrid nanocomposite properties are determined by using the Halpin-Tsai model. Going beyond the current field of application, the core layer is integrated with actuators and sensors, respectively at the top and bottom layers. The structure is controlled by a Proportional-Derivative (PD) controller, simulating real-world control mechanisms used in aerospace systems for flight safety. The structure is modeled by the nonlinear Refined Zigzag Plate (RZP) theory. The advanced numerical technique of the Differential Quadrature Hierarchical Finite Element Method (DQHFEM) for the solution of the motion equations provides a robust framework for studying the intricate flutter and aerodynamic behavior of the smart hybrid nanocomposite trapezoidal plates. The examination of the reliability of the structure employs the three-term conjugate finite-step length (TCFS) method. This technique is constructed through the utilization of the conjugate gradient method, incorporating a controlled scalar parameter to ensure numerical stability. The results of this article have been validated against existing experimental and numerical studies, demonstrating the validity of the presented model and the numerical technique used. The effects of various parameters, such as the smart controller, applied output voltage to the actuator layer, volume percentage of CNTs, agglomeration, and waviness of carbon fibers, geometric parameters, the skew angle of the plate, rupture, and yawed angle flow are examined on the flutter behavior, critical aerodynamic pressure, nonlinear frequency, and reliability index. The results indicate that the controlled system exhibits an approximately 18% increase in the flutter critical aerodynamic pressure compared to the uncontrolled system, along with a significant 50% rise in flutter frequency. Additionally, the structure with rupture displays approximately 20% lower flutter aerodynamic pressure and a 25% lower flutter frequency compared to a healthy plate. In the absence of carbon nanotubes and under positive external voltage, a damage parameter exceeding 0.35 leads to a reliability index below 0.931, indicating a risk of structural failure. Two solutions involve switching to negative voltage or increasing the volumetric percentage of carbon nanotubes, resulting in a 43% or 118% increase in reliability, respectively.