To better protect fresh groundwater resources, it is urgent to explore the hydrodynamic mechanism of seawater intrusion in coastal aquifers under complex hydrogeological conditions. In this study, a rigorous combination of laboratory experiments and numerical simulations was used to explore the mechanism of seawater intrusion under the combined influence of aquifer heterogeneity and tides. The results showed that spatial distribution of saltwater-freshwater in coastal heterogeneous aquifers was significantly different under the static and tidal sea boundaries. Tidal action reduced the intrusion distance of the saltwater wedge by 30.8%, resulting in a threefold increase in the width of the mixing zone around the saltwater wedge. Tidal action generated an upper saline plume (USP) in the intertidal zone, and fresh groundwater discharge was the key resistance to the accumulation of saltwater in the USP. When the flux of fresh groundwater discharge increased, the USP area would decrease. Under the same hydraulic gradient, the distance of seawater intrusion increased with the increasing permeability, regardless of static/tidal and homogeneous/heterogeneous conditions.