Resilience is especially important for a developing country such as China which aims to sustainable development. Previous studies mainly focused on a certain aspect of water resilience in some small-scale regions or watersheds, while systematic understanding and national-scale studies of that were rare. In this study, a new nature-society dual-structured water resilience index is developed to evaluate the capacity of water resource and environmental system in adapting to changes or disturbances and is applied in the case study of China at a national scale. The results indicate that the comprehensive level of water resilience in China was constantly improving in the past years, while the recent spatial distribution level in China was still not optimistic and differs greatly in some regions due to differentiated efforts in water resources conservation and governance. This study also identifies the serious resilience issues of China’s water resources system to provide reference for considering sustainability in national or provincial water resources planning and policy.