The study on ecological integrity has become an international hotspot. Improving the health and quality stability of aquatic ecosystem has been adopted as the ultimate management goal, direction and strategies worldwide. Since the “13th Five-Year Plan”, the quality of surface water has been significantly improved in China. However, the degradation, destruction and service function decline of aquatic ecosystem have been prominent shortcomings in typical watersheds. The overall conservation for physical, chemical and biological integrity should be emphasized for the future management of ecosystem. The amelioration of water quality and restoring the resilience and stability of aquatic ecosystem will be the vital goals and tasks for protection of freshwater ecosystems in China. In this review, the current status and demands for ecosystem conservation in typical watershed was firstly summarized. The significance of the researches of ecological integrity for fresh waters in China was elucidated. Then, the international progress and application practice of ecological integrity from foreign countries were demonstrated. The challenges and deficiencies were also highlighted for the present achievements of ecological integrity researches in China. Finally, the fundamental goal of this review was to guide the future developments and propose directions of ecological integrity studies in China. New technologies and methods for ecological integrity monitoring and assessment, degradation diagnosis, restoration and regulation should be expedited. The theories for multi-scale ecological integrity assessment need to be developed. Techniques for ecological integrity monitoring and assessment that integrates physical, chemical and aquatic biological metrics will be established in China. The ecological integrity assessment should be carried out periodically to grasp the ecosystem background and evolution trend for typical watersheds. The new methods for degradation diagnosis and restoration of ecological integrity need to be proposed to clarify the degradation mechanism and driving factors. It is also urgent to put forward the restoration pathway and regulation strategies for degraded aquatic ecosystems under the complex stress of climate change and human activities, which is beneficial to improve the scientificity, accuracy, and effectiveness for protection and restoration of freshwater ecosystem. Researches of ecological integrity are fundamental to speed up management and protection of aquatic ecosystem in China to enter to a new era, and to support the restoring and maintaining of freshwater ecosystems integrity and background.