Several saltwater influential factors including flow, tidal range, tidal level, sea level, climate, etc. at the two representative stations of Pinggang pump station and Lianshiwan station in Pearl River Estuary were researched, using set pair analysis and nonparametric correlation analysis methods. The results showed that: (1)In the Pearl River Estuary, the main influential factors to saltwater are flow, lowest tide level and the sea level. The tidal range and wind are secondary influential factors. (2)There are differences in the sensitivity of saltwater influential factors between Pinggang pumping station and Lianshiwan station. It is more sensitive to flow at Pinggang pumping station and more sensitive to sea level, the lowest tidal level, tidal range and the highest tidal level at Lianshiwan station. (3)The global climate continues warming, which makes low flow complex at the Pearl River Basin and sea level rising fast in the Pearl River Estuary. More research should be done on the changing mechanism of saltwater in Pearl River Estuary.