The application of sodium titanate anodes of low cost, feasible operating voltage, and nontoxic nature were severely hindered by their inferior cycling stability and poor rate capability. Here, three-dimensional (3D) chestnut-like NaTi3O6(OH)·2H2O@N-doped carbon nanospheres (NTOH@CN) with loose crystal structures were prepared by a self-sacrificed template method. The nanospheres were composed of nanosheets and linked with nanowires, which interweaved to construct a meshwork structure. The growth mechanism of unique 3D NTOH@CN nanospheres was investigated by tracking the synthesis process of different hydrothermal durations. The rate performances of 3D NTOH@CN were superior to that of NaTi3O6(OH)·2H2O irregular spheres assembled from nanosheets (3D NTOH) and NaTi3O6(OH)·2H2O nanosheets (two-dimensional NTOH). Excellent cycling and rate performance were obtained due to their open crystal structure, unique 3D nanosphere morphology with short diffusion paths, N-doped carbon surrounding, and the solid solution reaction. In addition, the reaction mechanism, morphology change, and dynamics research during the sodium insertion/desertion process have been carefully studied. Based on varying ex situ analyses, the irreversible metallic titanium formation and the excellent structural stability of nanosphere morphology have been evidenced. The pseudocapacitive phenomenon was also detected, which effectively enhanced Na+ ion storage capability. The systematical and comprehensive study provide a holograph for the design and synthesis of sodium titanate nanostructures.