The Second Tibetan Plateau Scientific Expedition and Research Program (“STEP Program”) has made significant progress in the world’s most influential frontier sciences. Based on the STEP Program, scientists are able to conduct theoretical and practical earth system science research that is fundamental to implementing exemplary solutions to basin protection (e.g., of atmosphere, water, and soil), restoration (e.g., of construction-disturbed areas, ecosystem degradation), and governance (e.g., of water environment degradation, land desertification, and soil erosion), particularly across ecologically fragile high-altitude areas. The Lhasa River Basin, located in the social and economic heartland of Tibet, encompasses the six spheres of earth system science and has been subjected to the dual substantial environmental impact from natural climate changes and human activities. Therefore, it is important to conduct fundamental applied scientific research on the protection, restoration, and governance of natural process-prevalent areas, natural process-human activity overlapping areas, and human activity areas. In this study, the Chabalang small watershed, a typical tributary in the Lhasa River Basin, was selected as the research object, and the effect of the early comprehensive governance demonstration area construction on the ecological environment of the watershed was systematically evaluated. The results showed that during the construction of the comprehensive demonstration area from 2010 to 2012, although the regional precipitation was low, the vegetation coverage in the basin significantly improved because of a series of engineering measures such as slope-to-terrace, artificial planting, and water diversion irrigation. The areas of severe soil erosion and mild soil erosion in the basin were also slightly reduced, according to the soil erosion intensity data for 2005 and 2015. There are several problems in the comprehensive demonstration area, such as lack of systematic observation (e.g., only automatic meteorological observation and slope runoff observation), lack of basic scientific research (e.g., the process and mechanism of runoff and sediment generation are unclear), lack of effective management (e.g., the equipment for automatic meteorological observation and artificial simulated rainfall observation are seriously damaged), and lack of comprehensive restoration and governance integration (e.g., the restoration and governance are scattered and disordered because of being conducted by different departments). Considering the existing problems in the comprehensive demonstration area, we propose a scientific solution to improve the scientific scheme of watershed protection, restoration, and governance. The technology system for protection, restoration, and governance in the Chabalang small watershed should include the protection of the atmosphere, water, and soil, the restoration of construction-disturbed areas and ecosystem degradation, the governance of water environment degradation, land desertification, and soil erosion. We present the following suggestions: improving the system of observation, research, and technology demonstration in the basin, strengthening the basic scientific research, establishing a multi-department coordination mechanism, and strengthening the application and popularisation of technology demonstration systems from the basin to the Tibetan Plateau. This will fill the gap in multi-dimensional observation research and provide a reference for the ecological environment of the Tibetan Plateau.