Abstract: In recent years, the saltwater intrusion in the the Pearl River Estuary has intensified, and the threat to the security of the basinal water supply is increasing. This paper focuses on the three major topographic changes of the Pearl River Estuary such as the riverbed downcutting in the network river area, the shringkage of the mouth sandbar in Modaomen Estuary, and the downcutting of the middle beach in Lingdingyang Estuary, and analyzes the quantitative impact of topographic changes on the upstream of saltwater intrusion tide in the Pearl River Estuary. The results show that compared to 1999, the upstream distance of the 0.5‰ salinity boundary in the Modaomen Waterway increased by 2.79 km due to the riverbed changes under the riverbed terrain of the network river area in 2016. After the mouth sandbar shrinkage in 2020, the maximum upstream distance increased by 5.3 km with the 0.5‰ salinity boundary in the Modaomen Waterway. The downcutting of the middle beach of Lingdingyang mainly affects the saltwater intrusion on the Dongjiang Delta, on the river channel in the Guangzhou area, and on the upstream rivers of Jiaomen and Hongqimen, but the upward distance of the salinity boundary is limited. Considering the influence of the three topographic changes, the saltwater intrusion distance increased to varying degrees in each river channel in the Pearl River Delta. The upward distance of the saltwater intrusion boundary in Modaomen Waterway is the largest, reaching 8.92 km. The salinity boundary along the Shawan and Shunde Waterway to Hongqimen has moved up 2.81 km and 2.02 km respectively. The salinity boundaries of other rivers have moved up between 1.02-1.85 km. This paper can provide reference for the prevention and control of saltwater intrusion and the security of water supply in the Pearl River Estuary.