With the rapid development of unmanned aerial vehicle (UAV) short-distance logistics transportation in urban scenarios, there is an urgent demand for the scientificity and safety of urban airspace planning, among which the efficient management and control of UAV route intersections constitutes one of the key technical bottlenecks. Taking the route intersections formed by the convergence of UAV routes as the research object, the core influencing factors of route intersection design were systematically sorted out, and the existing research progress and shortcomings were summarized. Furthermore, focusing on the typical scenario of controlled planar intersections, it was introduced the ground “traffic light”management concept, and combined the spatial characteristics of grade-separated intersections with the low-speed and low-altitude operational characteristics of UAVs, and constructs a general traffic model for logistics UAV intersections integrating virtual pipeline technology, traffic light control logic, and tidal layer dynamic scheduling mechanism. Additionally, a phase sequence scheme adapted to 3D airspace characteristics and a supporting optimized traffic light control strategy were designed. The proposed strategy was verified through simulation experiments, and the results show that the control strategy exhibits excellent performance in all traffic flow scenarios: in high-traffic scenarios, the traffic capacity of the intersection is increased by 47%, the average travel delay of UAVs is reduced by more than 30%, and the optimization effect is more significant in tidal traffic flow scenarios, effectively improving the operational safety and stability of the intersection. The research results provide theoretical support and technical reference for the planning and design of UAV route intersections and the optimization of management and control strategies in urban scenarios, and are of great significance for promoting the large-scale and standardized application of UAV logistics transportation systems.