This study analyzes how dynamic disturbances influence the decisions made during the human supervision of autonomous unmanned aerial vehicles. While previous research has primarily focused on control algorithms and system stability, the effect of disturbances originating from system dynamics on operator intervention behavior has been less extensively investigated. To examine this problem, a hardware-in-the-loop (HIL) experimental framework was developed, which is based on a previously validated unmanned aerial vehicles (UAVs) test platform and was adapted in this study to enable the investigation of human supervisory decision-making. Participants observed the behavior of an autonomously operating system under controlled disturbances and were provided with the possibility to intervene by activating an emergency landing mechanism. The results indicate that the disturbance intensity had a significant effect on intervention decisions, while the reaction times did not show notable differences. This finding suggests that supervisory behavior is primarily determined by the evaluation of the system state rather than by timing characteristics. It also identifies that subjective risk perception plays a decisive role in the formation of intervention decisions, indicating the presence of an implicit decision threshold for participant behavior. The research findings offer a novel approach to the interpretation of human–UAV interaction by emphasizing the role of system dynamics in shaping user decisions. The presented method may provide a foundation for the development of predictive and adaptive supervisory systems that take into account the characteristics of human decision-making, thereby contributing to the design of safer and more efficient autonomous systems.