Titanium dioxide (TiO2) is a promising negative electrode for sodium ion batteries (SIBs). Although TiO2 materials with amorphous (A-TiO2) and single-phase crystalline structures (C–TiO2) have been separately explored, the study to compare the fundamental electrochemistry of A-TiO2 and C–TiO2 is limited. In this work, we investigated A-TiO2 and C–TiO2 nanoparticles with identical chemical composition and morphology. C–TiO2 exhibits enhanced electrochemical performance than A-TiO2 in terms of rate capability and cycle life. Cyclic voltammetry (CV) analysis suggests reversible Na ion insertion/extraction in C–TiO2. However, such process is irreversible in the case of A-TiO2. The charge storage mechanisms in both samples were studied to show that diffusion-controlled intercalation process becomes significant in C–TiO2 sample. The C–TiO2 sample has a better Na+ diffusivity measured through the galvanostatic intermittent titration technique (GITT) compared to A-TiO2, which corroborates well with the rate capability study. Furthermore, the evolution of local structure of the TiO2 samples was analyzed by ex situ pair distribution function (PDF) to understand the variation in electrochemical properties. It reveals that the corner-shared Ti–Ti distance along Na ion diffusion pathway increases with the increase of crystallinity, leading to the expanded diffusion channels and therefore more active sites and faster diffusion.