The establishment of an accurate synthesis-structure-property relationship is the central scheme of materials science, which is particularly important for polymorphic materials possessing various structural forms with different properties. Manganese dioxide (MnO2) is a typical polymorphic material exhibiting various one-dimensional tunnel phases that are constructed by [MnO6] octahedra units, enabling its extensive applications in water desalination, (electro)catalysis and energy storage. Despite the long-range [MnO6] ordering confirmed by conventional diffraction tools, surprisingly, the electrochemical energy storage properties of a specific MnO2 tunnel phase still vary significantly in literature with unclear structural origins. Here, we demonstrate the existence of tunnel heterogeneity featuring localized tunnel intergrowths within single MnO2 nanoparticles via atomically-resolved imaging. Furthermore, combining both ex situ and in situ transmission electron microscopy, the tunnel heterogeneity within one MnO2 nanoparticle is demonstrated to significantly affect the energy storage kinetics in sodium ion battery even down to sub-nanometer scale. The origins of such tunnel structural heterogeneity in MnO2 are explored further, where a layer-to-tunnel (L-T) transition mechanism is identified to be responsible. The L-T transition is the essential step for the MnO2 layered precursors to gradually transform to tunnel polymorphs during the hydrothermal synthesis. The intermediate state during the L-T transition is successfully obtained and analyzed to extract the critical information regarding the atomic reconfiguration, compositional evolution and electronic structure change during this transition. It is found that the L-T transition is not homogeneous but rather topotactically happening from the layer edges into the body, which leads to the gradual splitting of 2D MnO2 layers into 1D nanowires possessing tunnel structure. The layers are transformed to 3×3 tunnels in multisteps via formation of intermediate tunnel phases exhibiting much larger openings. The transition starts by macroscopic layer distortion from adjacent Jahn-Teller active [Mn3+O6] octahedra, experiences Mn3+ disproportionation reaction and layer-interlayer Mn migration, expels doped Mg2+ out of the openings, and gradually builds the tunnels by reconstructing the Mn-O bonds. Findings in this work could guide the controlled synthesis and selective size-engineering of MnO2 tunnels for specific applications in various fields. We also expect it to call for renewed attention to the controlled synthesis of homogeneous tunnel-specific phases with predictable properties, and to yield a more precise structure-property relationship in polymorphic materials. Figure 1