Under the influence of sea-level rise caused by global warming and intensive human activities，salinity intrusion in the Pearl River Delta （PRD） has obviously intensified. It is necessary to analyze the main dynamic factors and the response trends of salinity intrusion. We establish a coupled 1D-3D coupled water salinity model，carry out the sensitivity test with the topography，upstream discharge at main station and sea-level rise changing respectively，apply the flux mechanism decomposition method to analyze the salt flux along the main streams of Xijiang River and Beijiang River，and discuss the response law of salinity intrusion in the estuary network to the change of main dynamic factors. The results show that the salt transport flux at all outlets are dominated by advection transport. Changes in topography and upstream discharge have a greater impact on the salt transport flux than the sea level rise. The salt transport flux increases less at the entrance after riverbed cutting and increases more in the upstream direction. During the spring tide，the advection transport and steady shear transport are mainly controlled by the upstream discharge at the main station to adjust the salt transport flux. During the neap tide，the tidal oscillatory transport for tide pumping is relatively large. The impact of sea-level rise on tide-dominated outlets （e.g. Hongqimen） is greater than that of river-dominated outlets （e.g. Modaomen），but the impact of sea-level rise in the short term is relatively small.