The seawater intrusion (SWI) process lasts for decades in real world, thus the research on dynamic process of SWI is essential. The freshwater-saltwater mixing zone plays a crucial role in governing the groundwater movement and the solute transport in coastal aquifers. To date, there has been a lack of research on the hydrodynamic behavior of the mixing zone in the presence of subsurface physical barriers. In this work, we employed laboratory experiments and numerical simulations to investigate the dynamics of the mixing zone, comparing scenarios with and without subsurface physical barriers. The findings indicate that the construction of a subsurface physical barrier will not immediately slow down the seawater intrusion velocity and change the salinity distribution of mixing zone. The block effect of subsurface physical barriers with different heights or bottom opening sizes became apparent only when the wedge toe approached the physical barriers. The widening effect of increasing longitudinal dispersivity on the mixing zone width was more pronounced during the dynamic process compared to the steady state. Furthermore, the widening effect of increasing longitudinal dispersivity on the mixing zone was more significant compared to transverse dispersivity in both the SWI and subsurface dam scenarios throughout the intrusion process. However, in the cutoff wall scenarios, the widening effect of increasing transverse dispersivity became more obvious during the later intrusion period. Our conclusions provide a reference for the groundwater management in coastal aquifers. According to the current seawater intrusion situation, the local water bureau can predict the seawater intrusion velocity and the temporal changes of mixing zone after the construction of physical barriers.