Manganese oxide is an effective active material in several electrochemical systems including batteries, supercapacitors, and electrochemical deionization (ECDI). This work conducts a comprehensive study on the ion-selective behavior of MnOx to fulfill the emptiness in the energy and environmental science field. Furthermore, it broadens the promising application of MnOx in the ion-selective ECDI system. With the support of a microfluidic cell and the electrochemical quartz crystal microbalance (EQCM) analysis, we proposed a time-dependent multi-mechanism ion-selective behavior with the following guidelines. (1) Hydrated radius is the most critical factor for ions with the same valence, and MnOx tends to capture cations with a small hydrated radius. (2) The importance of charge density rises when comparing cations with different valences, and MnOx prefers to capture divalent cations with a large hydrated radius but a strong electrostatic attraction. In addition, ion-swapping may occur where divalent cations replace monovalent cations in this circumstance. (3) NH4 + triggers MnOx dissolution, leading to performance and stability decay. The clear EQCM evidence has directly verified the proposed mechanisms. Moreover, the EQCM data provide a novel but simple method to judge ion selectivity preference. The overall ion selectivity sequence is Ca2+ > Mg2+ > K+ > NH4 + > Na+ > Li+ with the highest βCa//Li and βCa//Na values around 3 at the deionization time = 10 min.