Sodium-ion batteries (SIBs) are promising candidates for large-scale energy storage due to their cost effectiveness and the unlimited availability of sodium. However, there remains a need for the rational design of better anodic materials than are currently available, as these materials are critical for the sodium-ion storage process. In this work, theoretical calculations were performed to design a conceptually novel TiO₂@MoO₂ heterojunction (TMH) anode that was expected to exhibit better electrochemical performance than current anodes. The TMH anode was fabricated via a facile and cost–effective method, and the results of in-depth sodium-ion-storage performance and reaction kinetics analyses indicate that it exhibited an excellent rate capability and enhanced pseudocapacitive response, due to its high crystallinity. This electrochemical performance was superior to that of previously reported anodic materials, confirming the accuracy of the theoretical calculations. Destruction of TMH’s nanostructure at high temperatures resulted in a decrease in its electrochemical performance, indicating the key role played by the nanostructure in TMH’s ability to store sodium ions. This study demonstrates that integration of theoretical predictions with experimental investigations offers insights into how materials’ crystallinity and nanostructure affect their pseudocapacitive sodium-ion storage capabilities, which will help to guide the rational design of effective anodic materials for SIBs.