With the rapid development of urban air mobility, achieving safe and segregated flight for unmanned aerial vehicles amid the surging demand for low-altitude logistics has become a critical issue. This paper proposes a method for planning the public route network of urban low-altitude terminal logistics while considering environmental risks in the digital airspace. First, based on parallel system theory, we develop a digital airspace environment model that supports public route network planning by mapping physical and social elements to an artificial system. Furthermore, we establish a digital airspace grid partitioning system, develop grid access rules, and create a quantification model for urban low-altitude airspace environmental risks. Utilizing a layered airspace approach, this paper configures approach–departure grids, develops methods for initial public route network planning, and facilitates orderly re-planning of routes, ultimately establishing a hub-and-spoke public route network with segregation. This study conducts detailed case simulation studies based on realistic constraints, focusing on environmental risk, accurate grid configuration, comprehensive cost, algorithm complexity, and network scale. Simulation results demonstrate that the proposed method effectively constructs conflict-free networks, while maintaining low risks and inflection points. The findings align with the current development stage of urban air mobility characterized by the principle of ‘isolation first, then integration.’ This approach enables a gradual transition from route isolation to future integrated flight, thereby providing technical support for advancing low-altitude logistics operations.