This article presents a novel centralized control system for autonomous aerial vehicles that leverages a graph-based approach to prioritize safe, pre-planned, and collision-free navigation. With the prospective widespread adoption of Urban Air Mobility, the study focuses on integrating graphical structures into airspace management to ensure efficient and secure navigation for drones, UAVs, and flying automobiles, all of which possess unrestricted three-dimensional movement capabilities. The proposed dynamic navigation system is designed to adapt effectively to environmental changes and varying traffic densities, providing a robust framework to support the development and implementation of complex urban air mobility systems. The research underscores the potential of centralized control systems and graph-based structures in managing intricate aerial traffic, laying the groundwork for future studies to refine these cutting-edge technologies for real-world application. The simulation results demonstrate the system’s high efficiency in planning airspace routes, even with a large number of vehicles sharing the same space.