Abstract: As the core area of the "China Water Tower" and a crucial ecological security barrier for China, the Yangtze River source region is vital for the sustainable development of the entire river basin and the nation. To further enhance the systematic, scientific, and targeted protection and restoration of the aquatic ecosystem in the Yangtze River source region, this study analyzed the risks related to water quality, aquatic ecology, and water resources from an ecological security perspective, based on the findings from the joint research for the Yangtze River ecological environmental protection and restoration as well as literature review. It then identified their causes and proposed suggestions to strengthen ecological security risk prevention and control. The results indicated that although the overall water quality in the source region was excellent, fluctuations occurred at some national control stations during the active freeze-thaw period (May to September), posing challenges to stable compliance with water quality standards. The aquatic ecosystem exhibited a fragile structure with low biodiversity, and vegetation degradation risks existed in certain areas. The source region showed a clear warming and wetting trend, with a significant reduction in glacier area and increased instability in the water resource system. The main causes of risks included insufficient efficiency of sewage treatment facilities and difficulties in decentralized management, intensified ecological imbalance due to climate change, the incomplete establishment of a comprehensive governance system and long-term mechanisms, as well as inadequate research on baseline understanding and remediation. It was recommended to further advance the integrated protection and restoration of mountains, rivers, forests, farmlands, lakes, grasslands, and deserts, enhance ecological functions in core areas, establish and improve cross-basin ecological compensation and collaborative governance mechanisms, strengthen comprehensive governance capabilities, enhance scientific and technological support, develop localized governance technology systems and intelligent monitoring platforms, and achieve targeted prevention and control. This study provides a scientific basis for consolidating the ecological security barrier of the Yangtze River source region and ensuring the sustainable functioning of the "China Water Tower".