The new concept of Urban Air Mobility (UAM) and the emergent unmanned aerial vehicles are receiving more and more attention by several stakeholders for implementing new transport solutions. However, there are several issues to solve in order to implement successful UAM systems. Particularly, setting a suitable framework is central for including this new transportation system into the existing ones—both ground and aerial systems. Regulation and definition of aerial networks, but also the characterization of ground facilities (vertiports) to allow passengers and freight to access the services are among the most relevant issues to be discussed. To identify UAM transportation networks, suitably connected with ground transportation services, digital twin models could be adopted to support the modelling and simulation of existing—and expected—scenarios with constantly updated data for identifying solutions addressing the design and management of transport systems. In this perspective, a digital twin model applied to an existing urban context—the city of Bologna, in northern Italy—is presented in combination with a novel air transport network that includes the third dimension. The 3D Urban Air Network tries to satisfy the principle of linking origin/destination points by ensuring safe aerial paths and suitable aerial vehicle separations. It involves innovative dynamic links powered by a heuristic cost function. This work provides the initial framework to explore the integration of UAM services into realistic contexts, by avoiding the costs associated with flight simulations in reality. Moreover, it can be used for holistic analyses of UAM systems.