Effective environmental protection system is an effective way to promote the coordination between economic and social development and resources and environment. Based on the combing analysis of the development process of China’s environmental management institutions, systematically expounds the process of continuous improvement and change of the environmental management system. Combined with the characteristics of China’s economy from the stage of rapid growth to the stage of high-quality development, the key problems at present are analysed. Focusing on the demand of future ecological civilization construction and sustainable development, while on the basis of elaborating ecological security systematically, and then this paper puts forward the idea of optimum design of environmental protection system based on ecological security. According to the actual task of economic structure adjustment and economic layout adjustment under the construction of national ecological security, this paper focuses on improving the function of ecological services, and puts forward the countermeasures for optimizing the environmental protection system in China and the basic means for effective implementation of the safeguard system.