18-Crown-6 ether has attracted ever-increasing attention as the functional unit of biomimetic or smart nanomaterials for membrane separation, chemical sensing, and adsorption due to its outstanding ionic recognition performance. Most anomalous phenomena point to the close association between ionic recognition and the environment of aqueous solutions. However, the specific role of water molecules in ionic recognition by 18-crown-6 ether is poorly explained. In this work, we selected different single ionic species systems (K⁺, Na⁺, Li⁺, Mg²⁺, and Fe²⁺) and coexisting ionic systems (K⁺/Na⁺ and K⁺/Mg²⁺) to investigate the underlying mechanism of water molecules in the ionic recognition performance of 18-crown-6 ether by molecular dynamics simulation. Results demonstrated that ionic recognition followed the order of K⁺ > Na⁺ > Li⁺ > Fe²⁺ > Mg²⁺. Moreover, the selectivity of K⁺ recognition could be enhanced in the presence of Mg²⁺ than Na⁺. Detailed microstructural analyses demonstrated that the change in the hydrogen bond network structure of water molecules played a major assisting role in recognition. For K⁺, only the first hydration layer existed, from which water molecules can be easily removed. However, the strong electrostatic interaction between Fe²⁺ or Mg²⁺ and water molecules ensured that the orientation of water in the first hydration layer was unaffected by other hydration layers. In addition, comparing with the co-existing ion of Na⁺, the stronger competitiveness of Mg²⁺ resulted in the greater weakening of K⁺ hydration and lower energy requirement for water removal near the crown ether pore.