Alpha-MnO2 is an attractive cathode candidate for sodium-ion batteries attributed to its unique one-dimensional 2 × 2 tunnels for facile sodium-ion diffusion, in addition to its incomparable cost advantage. In particular, α-MnO2 shows superior rate capability with silver stabilizing ions at the center of tunnels that improve electrical conductivity. In this work, we directly compare structural transformation of silver-containing α-MnO2 nanorods (Ag1.22Mn8O16-x or L-Ag-HOL and Ag1.66Mn8O16-y or H–Ag-HOL), containing higher and lower concentrations of oxygen vacancies respectively, by transmission electron microscopy (TEM). The elaborate comparative and statistical TEM studies eliminate concerns regarding generalization errors and facilitate rational structural development of nanorods with improved functionality. It is found that sodium ions favorably diffuse through the area where oxygen vacancies are concentrated, and the samples with more silver ions and fewer oxygen vacancies (H–Ag-HOL) show more significant structural deformation with more inhomogeneous sodiation. The difference in functional electrochemistry coupled with the observed difference in inter- and intra-nanorod inhomogeneous structural evolution emphasizes the significance of the uniform electrical conductivity of the electrode. This work helps to improve the α-MnO2 electrode material for sodium-ion batteries as well as suggesting the importance of delicate statistical approaches for TEM investigations.