Building an ecological civilization lies fundamentally in establishing systems and mechanisms. General Secretary Xi Jinping emphasized that institutional construction must be regarded as the top priority in advancing the building of an ecological civilization. Since the 18th National Congress of the CPC, China has made remarkable achievements in the construction of the ecological civilization institutional system, major strides have been taken in the reform of the fundamental institutions for ecological civilization, the modernization of the reform of the ecological and environmental governance system has advanced in depth, major breakthroughs have been achieved in the reform of the green and low-carbon development mechanism; and an institutional system with the four beams and eight pillars structure for ecological civilization has basically taken shape. Based on China’s achievements in the construction of the ecological civilization institutional system in the new era, this paper focuses on the comparative analysis of the ecological and environmental protection system, efficient resource utilization system, ecological protection and restoration system, and ecological and environmental protection responsibility system, elaborating on the construction logic, operation characteristics and epochal value of the ecological civilization institutional system. From the perspective of construction logic, the ecological civilization institutional system is based on the value stance of ecology for the people, focuses on the practical needs of ecological civilization construction, strives to solve the difficulties in ecological governance, coordinates systems and the rule of law to consolidate the ecological defense line, and adheres to the practical orientation to carry out systematic institutional innovation. From the perspective of operation characteristics, the ecological civilization institutional system is a multi-level and all-round institutional mechanism driven by national administration, market mechanisms and comprehensive benefits. From the perspective of epochal value, the ecological civilization institutional system serves as an important guarantee for properly handling the five major relationships. Looking ahead, to thoroughly study and implement Xi Jinping Thought on Ecological Civilization, implement the Resolution of the CPC Central Committee on Further Deepening Reform Comprehensively to Advance Chinese Modernization, we should further improve the ecological civilization institutional system along the ideology-institution-practice path, form a Chinese governance model featuring the coordinated evolution of ecological rationality and institutional rationality, so as to provide a solid institutional guarantee for realizing the modernization of harmony between humanity and nature and for consolidating the ecological foundation for the sustainable development of the Chinese nation.