In this report, the electrochemical sodiation and desodiation in single crystalline alpha-MnO2 nanowires are studied dynamically at both single particle level using in situ transmission electron microscopy (TEM) and bulk level using in situ synchrotron X-ray. The TEM results suggest that the first sodiation process starts with tunnel-based Na+ intercalation, experiences the formation of Na0.5MnO2 as a result of tunnel degradation, and ends with the Mn2O3 phase. The inserted Na+ can be partially extracted out of the sodiated products, and the following cycles are dominated by the reversible conversion reaction between Na0.5MnO2 and Mn2O3. The Mn valence evolution inside a cycling coin using alpha-MnO2 nanowire electrode also exhibits partially reversible characteristic, agreeing well with the in situ TEM analysis. The sodiation is compared with lithiation in the same alpha-MnO2 nanowires. Both Na+ and Li+ interact with the tunneled structure via a similar tunnel-driven intercalation mechanism before Mn4+ is reduced to Mn3.5+. For the following deep insertion, the tunnels survive up to LiMnO2 (Mn3+) during lithiation, while the sodiation proceeds via a different mechanism that involves obvious phase transition and fast tunnel degradation after Mn’s valence is below 3.5+. The difference in charge carrier insertion mechanisms can be ascribed to the strong interaction between the tunnel frame and inserted Na+ possessing a larger ionic size than inserted Li+.