Cutoff walls are commonly used as an alternative to the desalination of coastal aquifers in many coastal regions. Current researches suggested that the high-velocity freshwater flow at the bottom cutoff wall opening was critical to prevent seawater intrusion (SWI). However, the role of the inland freshwater influx on coastal salinization is ignored. The groundwater cycle driven by the inland freshwater influx can be considered as a natural desalination process of coastal aquifers. Field-scale numerical models with the specified-head inland boundary and specified-flux inland boundary were used to investigate the effect of cutoff walls on the desalination of coastal aquifers. The results delineated that (1) both the freshwater flow velocity at the wall opening and inland freshwater influx significantly influence the seawater invasion length. (2) In contrast with the freshwater flow velocity at the wall opening, the inland freshwater influx is indeed the key factor controlling the desalination of coastal aquifers. The increase of inland freshwater influx narrows the freshwater-seawater mixing zone and reduces the groundwater salinization area. These results provide a comprehensive explanation on the hydrodynamic mechanism of cutoff walls and a reference for the groundwater resources management in coastal regions.