Climate change can have critical impacts on ecosystem services (ESs) and their inter-relationships, especially for water-related services. However, there has been little work done on characterizing the current and future changes in these services and their inter-relationships under a changing climate. Based on the revised universal soil loss equation (RUSLE), the soil conservation service curve number model (SCS-CN), and the improved stochastic weather-generator-based statistical downscaled global climate models (GCMs), we examined two important water-related services, namely, the soil conservation (SC) service and the flood mitigation (FM) service, and their inter-relationship under baseline and future climate scenarios (Representative Concentration Pathways (RCPs) 4.5 and 8.5). We took the Upper Hanjiang River Basin (UHRB), which is the core water source area of the China’s South-to-North Water Diversion Project (S–NWDP), as an illustration. The findings revealed that (1) the SC and FM services will both decrease under the two climate scenarios examined; (2) the SC and FM services showed a significant synergistic inter-relationship and the synergy will be improved by 16.48% and 2.95% under RCP 4.5 and RCP 8.5, respectively, which provides an opportunity for management optimization; (3) the ecological degradation in the UHRB will likely have serious consequences for the middle and lower reaches of the Hanjiang river basin, and therefore impact the actual economic benefits of the S–NWDP. This study points to the necessity for understanding the dynamic changes and inter-relationships of ecosystem services under future climate change and provides information regarding the consequences of climate change, which is useful for policy and infrastructure investment.