Salinity distribution depends strongly on estuary geometry, tidal amplitude, and freshwater discharge, which counteract salt intrusion. As an important part of the “New Western Land and Sea Corridor” in China, the Pinglu Canal Project (PCP) plan has been proposed to dredge a navigational channel from the Inland Qinjiang River to the Maowei Sea in South China Sea. Understanding the salinity transport process in estuary region is important for both water resource management and ecosystem health in the Qinjiang River Estuary (QRE). In this study, a predictive model of high-water slack was constructed based on the steady-state equation of salt intrusion, and the related measurable or quantifiable variables were considered through empirical relations. The developed model herein was applied to the QRE, and the predicted salt distribution appeared to agree well with the observations. Then, the response of fresh water discharge and tide on the process of salt intrusion in the QRE before and after the PCP construction was analyzed. The results indicate that when the water flow discharge is Q<100 m³/s, the saltwater intrusion length in the QRE during the high tide period can attach to 10–27 km after the channel deepening, increased by 4.5 km compared to the natural condition in a whole year, and the seawater will intrude to the Youth Ship Lock when the fresh water is Q<20 m³/s and tidal range is H₀>2 m. During the dry period, the Youth Hydro-hub can alleviate the saltwater intrusion by increasing the water discharge when the tidal range is H₀>2.0 m, and then decreasing the water discharge when the tidal range is H₀<1 m. The predictive model herein can be used to estimate the salt intrusion length under variable fresh water and tide level in the QRE region and provide efficient suggestions for quantifying upstream water discharge to mitigate salt intrusion after PCP construction.