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NaV₂O₅ mesocrystals were successfully synthesized from an alkaline-stripped pentavalent vanadium solution through a novel hydrothermal hydrogen reduction process. The optimal conditions for the hydrogen partial pressure, reaction temperature, initial solution pH value, and reaction time for the pure-phase NaV₂O₅ synthesis were ascertained to be 4 MPa, 200 °C, 4.0, and 2 h, respectively. The synthesis time (only 2 h) was greatly shortened, by nine times, compared with the most time-saving (18 h) hydrothermal process at present. X-ray diffraction (XRD) analysis revealed that the as-prepared powders demonstrated a typical layered orthorhombic structure of NaV₂O₅. The purity of the as-prepared NaV₂O₅ reached up to 99.98%. An electrochemical test showed that the as-prepared NaV₂O₅ has a potential application in sodium ion batteries. According to scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses, the as-prepared NaV₂O₅ powders were identified to have rod-like mesocrystals consisting of small rods which preferentially grow along the (010) direction. Furthermore, the phase transformation mechanism and crystal growth mechanism in NaV₂O₅ preparation were discussed systematically, based on which the synthesis mechanism of NaV₂O₅ was proposed as pentavalent vanadates pre-sedimentation, hydrogen reduction with dehydration, sodium ions insertion, and finally self-assembly oriented attachment. The synthesis process is characterized as time-saving and low-cost, and thus it may have great application prospects.