The Water Diversion Project from the Three Gorges Reservoir to the Hanjiang River (WDTGH) is a follow-up project to the Middle Route Project (MRP) of the South-to-North Water Diversion (SNWD). During the feasibility study stage, four routes of water conveyance tunnel under the Danjiangkou dam were proposed for comparison based on their topographical and geological conditions and engineering geological problems. The geological conditions of the proposed routes are complex, with long routes, large burial depths, varied formation lithology, abundant dissolvable rocks and soft rocks, complex geological structure background, and high overall geostress levels. Therefore, it is necessary to select a route with relatively good geological conditions to avoid engineering geological problems that may occur in the deep-buried long tunnel project. Through analysis, the geological factors considered in the comparison and selection of the routes were classified into three levels as key geological factors, important geological factors, and general geological factors. A comparison model under the condition of multiple factors was established for comprehensive analysis and comparison on engineering geology. The study reveal that the water tunnel scheme of Long'an Line 1 has overall advantages. Thus, the results of geological route selection provide foundation for comprehensive route selection in engineering design. Additionally, the research ideas and methods of geological comparison and selection can serve as a reference for similar projects.