Rural domestic sewage, originating from human activities that involve the extraction and utilization of natural resources, is an inherent component of the ecological cycle in nature. Therefore, its disposal methods should align and harmonize with the laws governing nature’s evolutionary processes. This study conducted a comprehensive investigation on the domestic sewage facilities in representative villages located within the water source protection area of the middle route of the South-to-North Water Diversion Project. Taking Village A’s domestic sewage treatment station as a case study, an analysis was performed to assess its operational status and identify existing issues. The consideration of rural domestic sewage treatment should encompass factors such as the generation and discharge of household wastewater, the characteristics of water quality, discharge regulations, the natural and social environment, as well as post-completion operations and maintenance modes. We also proposed source reduction measures for the reuse of gray water in domestic sewage treatment in Village A, along with integrated treatment approaches involving biochemical treatment, landscape integration, and farmland irrigation for black water. These measures not only achieve effective treatment outcomes but also foster harmonious coexistence between humans and nature. Moreover, they align with the principles of ecological civilization while considering rural revitalization and promoting green agricultural development.