The ecological and environmental issues associated with river basin have received worldwide attention, and in China, the problems associated with river basins urgently require solutions. By promoting the integrity of watershed ecosystems, the concept of community of shared life composed of mountains-rivers-forests-farmlands-lakes-grasslands is of great significance to the ecological protection and restoration of river basins in China during the new era. In the present study, the Minjiang River basin (Fujian Province, China), which is a national pilot project area for ecological protection and restoration was concerned. Based on the introductions to its ecological-environmental conditions, and the importance of regional ecological functions within the Minjiang River basin via literature review and analysis, the overall ecological security pattern composed of the river, riparian zones, mining areas, and ecological barriers were proposed. The present study also revealed a series of related threats, such as river pollution, riparian hillside soil erosion, mining destruction, forest barriers, and biodiversity degradation. Considering the ecological security pattern and current ecological-environmental issues, the present proposes major tasks and corresponding engineering measures, including the treatment of water in the Minjiang River, management of soil erosion along riparian zones, repair of abandoned land within mining areas, protection of forests and biodiversity in the Wuyi Mountains and other important ecological barriers, thereby reflecting the integrated and systematic requirements and intrinsic logic for basin protection and restoration. Supporting measures such as monitoring and evaluation are also discussed. This study provides a scientific basis and practical experience for improving ecosystems in the Minjiang River basin and for implementing national projects of ecological protection and restoration in China.