Water resource is the focus and hinge between ecological environment and socio-economic development. Watershed is the basic unit of hydrology and water resource studies. It is the current hotspot in water science research to carry out the integrated research of the hydrology and water resource at the watershed scale. The Heihe River Basin is the second largest inland river basin in northwestern China, which becomes one of the hot watersheds for its unique hydrological and geographical characteristics. Based on the Web of Science Core Collection, the scientific advances achieved in the Heihe River Basin were estimated from the new sight by combining disciplinary development and problem focus, time evolution and spatial variations. The results indicated that the Heihe River Basin has made positive contribution to the world science in remote sensing, evapotranspiration, water cycle, water resources management and utilization, and climate change research in arid areas. The great achievements has promoted the Heihe River Basin up to the same levels as the international typical basins in the past 30 years, especially after the performances of the major research program entitled “Integrated Study of Eco-hydrological Processes in the Heihe River Basin” (referred to as “Heihe River Program”) supported by a grant from the National Natural Science Foundation of China and large field observation experiments. The number of published articles has ranked the top 20 in the global watershed science research. Some important scientific achievements have been obtained at the mechanisms of eco-hydrological processes in inland river basins, which can actively serve the decision making of the water resource management and sustainable development in the Heihe River Basin. The data mining and contrastive study based on bibliometrics can afford scientific reference for the watershed science research.