Manganese dioxide, in particular α-MnO2, is one of the advanced inorganic nanomaterials having wide applications in many areas. Hence, understanding the crystallization pathways, morphologies, and formation mechanism of defects in its structure is of particular importance, not only for fundamental science but also for practical applications. Herein, different physically and chemically based methods, such as Neutron Diffraction (ND), XRD, SEM, TPR- H2, TGA-DSC, FT-IR, Positron Annihilation Lifetime (PAL), Doppler Broadening (DB) of positron annihilation radiation, and Electron-Momentum Distribution (EMD) measurements combined with theoretical calculations, were utilized to systematically investigate the composition, structure, and morphology of α-MnO2 nanomaterial under different annealed temperatures. The investigated material was synthesized at room temperature using a facile chemical method with potassium permanganate (KMnO4) and ethanol (C2H5OH), prior to being treated by temperatures of 100 oC – 800 oC. Results demonstrated, for the first time, that the α-MnO2 nucleation can be formed even at room temperature and gradually developed to α-MnO2 nanorods at 600 oC. This novel finding, which cannot be explored by conventional XRD, was confirmed by ND analysis. In addition, PAL analysis combined with theoretical ab initio calculations indicated the existence of H+ ions in the tunnel [1x1] of α-MnO2. At the same time, DB and EMD measurements explored the presence of Mn and O vacancies in α-MnO2 crystals at low temperatures. Finally, the present study reported a remarkable finding that organic molecules may act as reactants as well as templates, which are entirely decomposed and disappeared at highly annealed temperatures.