Manganese oxides are attracting great interest owing to their rich polymorphism and multiple valent states, which give rise to a wide range of applications in catalysis, capacitors, ion batteries, and so forth. Most of their functionalities are connected to transitions among the various polymorphisms and Mn valences. However, their atomic-scale dynamics is still a great challenge. Herein, we discovered a strong heterogeneity in the crystalline structure and defects, as well as in the Mn valence state. The transitions are studied by in situ transmission electron microscopy (TEM), and they involve a complex ordering of [MnO6] octahedra as the basic building tunnels. MnO2 nanowires synthesized using solution-based hydrothermal methods usually exhibit a large number of multiple polymorphism impurities with different tunnel sizes. Upon heating, MnO2 nanowires undergo a series of stoichiometric polymorphism changes, followed by oxygen release toward an oxygen-deficient spinel and rock-salt phase. The impurity polymorphism exhibits an abnormally high stability with interesting small-large-small tunnel size transition, which is attributed to a preferential stabilizer (K+) concentration, as well as a strong competition of kinetics and thermodynamics. Our results unveil the complicated intergrowth of polymorphism impurities in MnO2, which provide insights into the heterogeneous kinetics, thermodynamics, and transport properties of the tunnel-based building blocks.