The adoption of both Nature-based Solutions (NbS) and a system perspective is a hot issue and an area in which there is much room for improvement in ecological protection and restoration. The study takes Altay region as an example, an area located in Xinjiang, China, which is an important ecological corridor of the national key functional area and the core area of the Belt and Road but has a fragile ecological environment and needs much enhancement in ecological protection and restoration. Guided by the concept of “mountains-rivers-forests-farmlands-lakes-grasslands (MRFFLG) system is a life community”, the coupling relationship of the various MRFFLG elements, the main ecological environmental problems and the integrated countermeasures for protection and restoration in Altay region have been analyzed in this study. The study shows that Altay region has a typical meta-ecosystem of mountain, oasis, and desert, and the connections by rivers and lakes make the ecosystem links within the region much closer. The interweaving of resource-environmental-ecological issues of the aquatic ecosystem, degradation of the quality of terrestrial ecosystems such as forests, grasslands and farmlands, the increased ecosystem fragmentation and ecological risks are the major ecological environmental issues in this region. This study takes the improvement of the ecosystem health and function in Altay region as the core goal of regional ecological protection and restoration. First, we establish a zoning governance pattern from the perspective of ecosystem integrity; second, we design governance strategies for different zones with the goal of synergistic improvements in the ecosystem functions; and finally, we clarify the key engineering tasks in different zones from the perspective of ecosystem services. Ecological conservation and restoration of the MRFFLG system is a prime example of the application and development of NbS in China. This paper constructs an analytical framework for identifying regional life communities, diagnosing ecological protection and restoration of zoning problems, and proposing classified solutions for ecological protection tasks for the protection of the MRFFLG system. This research will enrich the theory and technology for the protection and restoration of MRFFLG systems, and provide guidance for the practice of ecological protection and restoration in Altay region.