This paper presents an assessment framework that analyses the impacts of climate change on the water diversion strategies of a water transfer project in China. A water diversion strategy consists of high and low water levels as well as related diversion flows in four operating periods: pre-flood, flood, post-flood and non-flood periods. The optimal water diversion problem is defined as a multi-objective problem with two conflicting objectives: minimising human and ecological water supply shortages, and solved by the popular non-dominated sorting genetic algorithm II (NSGA-II). The derived Pareto-optimal solutions are then evaluated using the predicted runoffs based on an ensemble of three general circulation models under three climate scenarios. Results obtained from the study catchment show that intra-annual distribution of future runoff changes. The optimal solutions on the Pareto front have greatly varying performance under a climate scenario. It is critical to reveal the different impacts of climate change on the water shortages over the four operating periods, in particular when an increase of water shortage in one period is masked by a reduction in one or more periods. This study illustrates that the framework can be used to identify resilient water diversion strategies to mitigate the potential impacts of climate change on the operation of a water transfer project.