Water security is the basis of sustainable human development. A new evaluation system of water security was established based on the natural–social dualistic water cycle theory, and then applied to characterize water security issues in China. At the national scale, the current state of water security was moderate, which was attributed to the improvement of water resource management level. However, it is still seriously inadequate in coordination of water use between ecological protection and socio-economic development, and wastewater treatment and reuse. Consequently, a resilient and integrated water management with adaptive capacity is needed. Moreover, the water security state in southern China was better than that in northern China, which was mainly attributed to the abundance of water resources in the south. Although the critical factors hindering water security were significantly different among China's 31 administrative regions, the low urban sewage reuse rate was a common factor, and irrigation efficiency was low in most parts of southern China. While in northern China, water resource overexploitation, polluted water quality and degraded aquatic ecosystems were common challenges. The results are consistent with the actual situations of China, and the related analysis can provide a reference for increasing regional water security.