Saltwater intrusion in the Yangtze Estuary is a natural phenomenon that often occurs in dry seasons, but it's particularly more terrible in early 2014 compared to previous years. This paper analyzed the basic situation of the saltwater intrusion and its formation reasons, discussed the mechanism and invasion pathways of saltwater intrusion in the Yangtze River estuary. Furthermore, combined with historical data, this paper analyzed the new features of saltwater intrusion that appeared in the Yangtze River Estuary in new situation. On the basis and from points of water source place, technical measures, water resources management and unified deployment of the Yangtze River, this paper discussed how to effectively deal with the effect of saltwater intrusion on public water supply in the Yangtze River Estuary.