With the advent of Anthropocene, the development of science and technology has made the man-land relationship increasingly close, and the contradiction between human and nature has become more and more obvious. Nowadays, how to deal with the relationship between socioeconomic development and environmental protection is at the top of the agenda of China as well as the rest of the world. In order to solve the problem that only one single element or only one type of ecosystem were considered in the traditional ecological conservation and restoration projects, China launched the mountains-rivers-forests-farmlands-lakes-grasslands ecological restoration projects in 2016 aiming to manage all kinds of ecosystems in a holistic, systematic and comprehensive way, which requires the active participation, common protection, and joint management of interested parties in various departments. At the same time, the guidance of scientific and systematic ecosystem theories and methods is also the premise for successfully and smoothly implementing these ecological restoration projects. And the final goal of the projects is to maintain the integrity of all kinds of ecological elements, and keep the resistance, resilience, and self-organization ability of ecosystem in good condition. However, there are still some problems in the process of current environmental governance, such as poor understanding of the concept and mechanism of coupling within and between different systems, insufficient attention to "scale", and lack of scientific analysis methods, which have restricted the effectiveness of protection and restoration. In this regard, the concept of coupling in the field of ecology, the mechanism of coupling within and between different systems, and models and methods that have been applied in the researches on coupling on three scales were introduced and summarized in this research. Then, the Shule River Basin, a national key glacier water conservation area and a priority area for biodiversity conservation, as well as one of the pilot areas of mountains-rivers-forests-farmlands-lakes-grasslands ecological restoration projects, was taken as an example to analyze the coupling relationship between ecological elements and between systems by applying the models and methods mentioned earlier. Finally, based on the case study, a multi-scale coupling analysis framework and an "up-scale" conservation and restoration pattern from the coupling perspective were proposed to help relevant decision makers to clarify the coupling relationship between ecological elements and between systems in Shule River Basin and other pilot areas, to enhance the scientific rationality and effectiveness of the overall environmental governance, and to promote the sustainable development of our society and environment.