UAVs will present significant air traffic in the urban airspace in the future, which brings new challenges to urban air traffic management and control. This paper presents an air route design scheme for multi-rotor UAVs in urban airspace to enable UAV operations at orderly levels. The air routes include legs and intersections, which are the three-dimensional channels of UAV flight. Based on the concept of structured and layered urban airspace, the cylindrical pipeline flight leg is designed, and the operation concept, characteristic parameters and flight procedures of along-road and roundabout intersections are proposed. By defining UAV conflict risk and intersection service level metrics, the operation situation of UAVs is quantitatively evaluated. Taking an urban transportation scenario as a case, the proposed route design scheme is simulated in different scale UAV operating scenarios. The results show that the number of UAVs at the intersection is positively correlated with the conflict probability, the number of crossing routes is negatively correlated with the intersection passing rate, and the UAV arrival rate is positively correlated with the intersection average passing time. The along-road type intersection is suitable for the area with fewer crossing routes and sparse UAVs, while the roundabout type intersection is adapted for the area with more crossing routes and dense UAVs. This research provides a new idea for urban UAV air route design, which is helpful in promoting the standardized management of UAVs and accelerating the integration of UAVs into urban airspace.