The research of the fate of river-sea transport system of Taiwan, consisting of three independent projects, FATES-KP, FATES-COMMARC and FATES-HYPER, is an integrated scientific project from a source-to-sink perspective. The three projects have been implemented one after another from 2003. Up to now, it has undergone nine years and a lot of important results have been obtained. The research intended to investigate the working of a material dispersal system consisting of a small mountainous river, a narrow shelf, and a nearby submarine canyon in a tectonically active setting that is also influenced by the monsoon climate. Along with the advance of the project, the research area gradually expanded to the north of South China Sea, Taiwan Strait and Okinawa trough. The project takes the lead of source-to-sink research of the South China Sea. This paper reviews the research methods, contents, main achievements and problems during the project in order to provide some helpful suggestions to the source-to-sink research of South China Sea of Mainland.