The capacity fluctuation phenomenon during cycling, which is closely related with solid electrolyte interphase and plays a key role for the design for advanced electrode, could be frequently observed in the titanium-based anode. However, the underlying reason for capacity fluctuation still remains unclear with rare related reports. Here, the origin of capacity fluctuation is verified with a long-life Na2Ti6O13 anode. The reaction mechanism, structural evolution and reaction kinetics during the reported sodiation/desodiation processes were carefully investigated. The gradually enhanced diffusion controlled contribution resulted in the capacity increasing. And the capacity decay could be ascribed to the irreversible reaction of metallic titanium formation and the increasing potential polarization. It is worth noting that sodium ions seem to partially reduce NTO to metallic state, which is irreversible. The present study can provide more information for the design of advanced Na2Ti6O13 anode.