To investigate the characteristics and laws of saltwater intrusion in the Yangtze River estuary, a 2D mathematical model of flow salinity in a wide scope covering Yangtze River estuary, Hangzhou Bay, and Zhoushan islands is established according to tidal hydrological data of the Yangtze River Estuary in March 2002 during dry season. Results suggest that in temporal scale, the salinity in some water areas of the south branch reduces to valley at spring tide while reaches peak at ebb opposite to general regularity due to the saltwater flowing backward from the north branch; in spatial scale, the distribution of salinity in the south branch displays a pattern of “high-low-high” during spring tide, and the salinity in the entrance at tide is significantly higher than that at ebb. Numerical analysis results are consistent with model test data. Moreover, tidal diameter dynamic analysis for the north branch reveals that a bigger tidal range in open sea leads to smaller upstream runoff and larger possibility of saltwater intrusion into the south branch from the north branch, which indicates that the diversion ratio at north branch increases exponentially with runoff in the upper reach, but is inversely proportional to tidal range.