A scientific investigation in the source area of Yangtze River and Lancang River was carried out by Changjiang(Yangtze) River Scientific Research Institute(CRSRI) in 2012. The investigation covers topics inclusive of river channel morphology, hydrology and sediment, water resource variation and exploitation, current status and causes of soil-water loss, water environment and water ecology, as well as geology and geomorphology. In the present paper, the whole process of the investigation is presented, with emphasis on the targets, significance, tasks and contents, and organizing pattern as well. Experiences and defects are summarized in aspects of topic and participants selection, investigation scheme and technical preparation, route selection, health condition, and logistic support for large-scale scientific investigation on the plateau. Suggestions are put forward for reference for similar scientific investigations.  