The Loess Plateau of China is one of the regions with the most serious soil erosion globally. The ambitious “Grain for Green” project was there implemented to restore degraded ecosystems, profoundly changing the water yield and carbon sequestration ecosystem services. To understand the changes of water- and carbon-related ecosystem services (hereafter WCES) in the Loess Plateau, this study combined the CASA (Carnegie-Ames-Stanford Approach) model and InVEST (Integrated Valuation of Ecosystem Services and Trade-offs) model to thoroughly reveal the changes and intrinsic linkages of water yield and net primary productivity since the “Grain for Green” project in the Loess Plateau. The results show that the WCES of the Loess Plateau were increasing since 2001, dominated by both the climate change and human afforestation. The water yield and net primary productivity showed strong synergistic effects in 80% of the Loess Plateau, mainly resulting from the rapid increase of precipitation in recent years. The increasing atmospheric precipitation contributed to more WCES provisions, which may have offset the trade-off between WCES caused by large-scale afforestation. In view of the synergistic effects of WCES, enhancing water input into the ecosystem may be an effective measure to respond with future WCES degradation in dry years, such as artificial basin-cross water transfer project. Despite the low correlation between teleconnection factors and WCES, the low water yield and reduction of net primary productivity may be associated with a strong El Niño event in 2015. This study assists in a wise decision-making on the future “Grain for Green” and ecological management in the Loess Plateau.