The long passageway in mountain city has the characteristics of complex terrain conditions, long mileage, many control factors and large engineering investment. In the context of the implementation of the "three regions and three lines" in the territorial spatial planning, the route selection stage should be well coordinated with the "three regions and three lines" in advance, and the intensive use of land and other resources. Aiming at the characteristics of long passageway in mountain city, the method and principle of route design are analyzed. Taking Chongqing Central City - Qiwan Express Passage Project as an example, 3D GIS technology is used to establish a basic model based on a wide range of terrain data, the 3D visualization simulation analysis of route scheme is carried out, and the demonstration example of route selection and spatial collaboration of long passageway in mountain city is analyzed.