As an important part of Xi Jinping's thought on ecological civilization, to adopt a holistic approach to conserving our mountains-rivers-forests-farmlands-lakes-grasslands has important guiding significance for ecological protection and restoration practices in China. In the present study, taking the Three Gorges area of Hubei Province as a case study, we firstly described the system principles of life community and analyzed major eco-environmental problems in this area. Then, the overall design and objectives for ecological protection and restoration were explored from the perspectives of watershed ecology and ecosystem integrity. We further proposed that some specific measures could be implemented from the following aspects:(1) comprehensive treatment on water environment and soil erosion; (2) ecological restoration on the shoreline of the Yangtze River, contaminated land, abandoned mines, as well as rivers and lakes; (3) protection of endangered animals and plants in the Three Gorges area; (4) construction of eco-agriculture demonstration zones along the rivers; and (5) innovation in environmental management mechanisms. These measures may be helpful for developing a unique protection and restoration system featured with "overall protection, integrated restoration, comprehensive management, regional association, and multi-departmental cooperation". Therefore, our research provides not only a scientific basis for ecological protection and restoration practices of the mountain-river-forest-farmland-lake-grasslands system in the Three Gorges area, but also a demonstration pilot for other regions.