At present, the problems of lake eutrophication and cyanobacterial blooms in China are still very prominent and the state attaches great importance to the ecological environment protection of lakes. Since the "Ninth Five-Year Plan", the government has started to control the "old three lakes" of Lake Taihu, Lake Chaohu and Lake Dianchi, but it has spent huge treatment costs. After nearly 30 years of governance, the trend of further deterioration of water quality in the "old three lakes" was initially curbed. According to the degree of lake pollution, lake control and protection can be divided into three types:"pollution control type", "combined prevention and control type" and "ecological conservation type". The governance of the "old three lakes" was a typical "pollution first, treatment later" model, and the lakes with better water quality mainly belong to "ecological conservation type", so the treatment model for "old three lakes" is not suitable for the protection of lakes with better water quality. This paper systematically summarizes the formation of the concept of priority protection of lakes with better water quality in China and the implementation history of special lakes with better water quality. According to the characteristics of the lake with better water quality and the general process of ecosystem degradation and restoration, the basic idea for the protection of the lakes with better water quality was put forward. From a thermodynamic perspective, the entropy increase process of nitrogen and phosphorus nutrient input into the lake ecosystem was analyzed, revealing the root cause of the degradation of the lake ecosystem and the importance of source control of nitrogen and phosphorus pollution load into lakes. The ecological security pattern of lake basin is the basis for ensuring the health of lake basin ecosystem. From the perspective of landscape ecology, this paper clarifies that optimizing the use of soil and water resources in lake basin and optimizing the development pattern are important ways to reduce the environmental pressure on the lake. The transition process of the "clear water state" dominated by submerged plants and the "turbid water state" dominated by phytoplankton in shallow lake ecosystems is not along the same pathway. There are upper and lower critical thresholds, and the aquatic ecological restoration process shows a hysteresis phenomenon. From the theory of steady-state transformation of lake water ecosystem, we clarified that the lake ecological restoration project should be implemented before the degradation transformation of lake ecosystem to obtain higher protection benefits. The support of 81 lakes with better water quality through the special national finance can not only promote the economic and social development of the lake basin, but also ensure the improvement of the quality of the lake water environment and improvement of lake water ecosystem. We recommended to strengthen the summary of different types of lake protection models, conduct in-depth research on the theory of ecosystem succession and protection technology of lakes with better water quality, and support the state to carry out the protection of lakes with better water quality systematically.