The outstanding ionic sieving capabilities of the nanoporous membranes have been evident; however, the selectivity in mixed solutions is often lower than that in single salt solutions. Given that the inherent properties of nanochannels remain the same, the ionic coordination structure in mixed solution becomes a remarkable factor for the inferior selectivity, and may change due to the interaction between anions and multivalent cations, a phenomenon rarely explored. Herein, molecular simulations demonstrated some free hydrated ions transfer to ionic clusters consisting of multi‐ions in representative LiCl/MgCl2 mixed solutions, and the ionic permeability discrepancy is exponentially associated with ionic cluster change. Ionic clusters are engaged by the enhanced coordination of chloride ions under the interference of divalent cations. Hence, by introducing anions with weak coordination ability, this detrimental effect is mitigated and ion selectivity is improved. This work provides essential theoretical foundations for further ion sieving applications in complex system.