Based on a one-dimensional salinity advection-diffusion model, an analytical expression for the salt flux transport mechanism in a regular semi-diurnal tidal estuary was derived. The effects of factors such as runoff, salinity, tidal amplitude, tidal current amplitude, phase difference between tidal current and tide, water depth, and estuary width on salinity diffusion were analyzed, quantitatively revealing the physical mechanism of the saltwater intrusion process in tidal estuaries. Furthermore, this analytical solution was utilized to explain the importance of each component of the salinity transport mechanism in Humen of the Pearl River Estuary. The results show that the Eulerian transport mechanism is controlled by upstream runoff; the Stokes drift transport mechanism is controlled by the tidal amplitude, tidal current amplitude, and their phase difference, and the tidal pumping effect is the result of the interaction among tidal pulsation, tidal current pulsation, and salinity pulsation; during the neap tide period in Humen, the semi-diurnal tidal characteristics are prominent; the advection transport is the main dynamic mechanism; the Eulerian residual flow transport is dominant, and the tidal pumping effect is not obvious; except for the mouth area, the salt flux generally shows a seaward transport trend during the tidal cycle; local areas of Humen are controlled by the tidal trapping mechanism, and between Zhangpeng and Machong stations, the downward discharge of saltwater is obstructed, which further intensifies the saltwater intrusion phenomenon in Humen.