The South-to-North Water Diversion Project has been in operation since 2014, directly benefiting more than 79 million people in China. Thus, its service life and long-term performance have gained much attention from scholars. To predict its life and performance, this study used the seepage/stress-damage coupling method. In addition, a seepage/stress-damage coupling theory was proposed and a finite element model of a deep excavated canal in the Xichuan Section of the South-to-North Water Diversion Project was established. The results showed that this canal subsided greatly in the first two years of operation, which can be confirmed by the monitoring data. It is predicted that, after 50 years of normal operation, the canal damage may start and spread from the water level, and reach 37.6%, but such damage will not affect its normal water delivery function. The purpose of this study is to provide guidance for the safe operation of the project.