Hard carbons, due to their relatively low cost and good electrochemical performance, are considered the most promising anode materials for Na-ion batteries. Despite the many reported structures of hard carbon, the practical use of hard carbon anodes is largely limited by low initial Coulombic efficiency (ICE), and the sodium storage mechanism still remains elusive. A better understanding of the sodium-ion behavior in hard carbon anodes is crucial to develop more efficient sodium-ion batteries. Here, a series of hard carbon materials with tailored morphology and surface functionality was synthesized via hydrothermal carbonization and subsequent pyrolysis from 1000 to 1900 °C. Electrochemical results revealed different sodiation-desodiation trends in the galvanostatic potential profiles and varying ICE and were compared with theoretical studies to understand the effect of the varying hard carbon structure on the sodium storage process at different voltages. Furthermore, electrode expansion during cycling was investigated by in situ dilatometry; to the best of our knowledge, this is the first time that the technique has been applied to hard carbons for ion storage mechanism investigation in Na-ion batteries. Combining experimental and theoretical results, we propose a model for sodium storage in our hard carbons that consist of Na-ion storage at defect sites and by intercalation in the high voltage slope region and via pore filling in the low voltage plateau region; these findings are important for the design of future electrode materials with high capacity and efficiency.