The Yellow River is China's second largest river with a drainage area of about 800,000 km2 and it has been seen as a cradle of Chinese civilization. Now it serves as one of the main theatres for the on-going national campaign to develop the western hinterland of the country. The river basin lies mainly in the semi-arid and semi-humid climatic zones where water resources are congenitally deficient. Per capita water volume in the basin is less 1/3 than that of national average. Due to the impact of both warm-dry scenarios of climate and human activities, frequent dried-up of its lower reach main-courses and main tributaries have occurred in the last 30 years. The ominous development not only aggravates the fragile balance of water demand and water supply in the-basin, but also brings in more impacts on the native eco-system and the environment along the river's reaches. The river's harnessing used to be a state affair of vital importance for a national stability in terms of national security. Since 1999, the Ministry of Science and Technology of China has set up a five-year project in the National Development Program for Key Basic Science Research, as is called “973 Program”. The author of this paper, as chief scientist of the project, summarized major research outcomes on the basis of about 800 papers and tens of monographs published recently. A stack of the research achievements from the project can be recapitulated by three kinds of the highlights, namely progresses in theory, technology and application to the Yellow river.