NASICON-type Na3V2(PO4)2F3 is employed as a promising cathode for sodium-ion batteries in order to explore the ion-migration mechanism and diffusion capability. Two kinds of Na sites, namely Na(1) site and Na(2) site exist in the crystal structure per formula unit to accommodate a total of three sodium ions. The ion at Na(2) site with half occupation extracts first and inserts the last due to its high chemical potential, while the whole extraction/insertion of two ions between 1.6 and 4.6 V vs. Na+/Na can produce three plateaus in charge/discharge processes because of the reorganization of ions. The first discharge capacity of 111.6 mAh g−1 with retention of 97.6% after 50 cycles could be obtained by electrochemical testing at 0.091C. Electrochemical activation and/or structural reorganization of the system by cycling could improve the diffusion coefficient of sodium with a comparatively large magnitude of 10−12 cm2 s−1, though many influences on the resistance factors also can be attributed to the cycling process. Such work is of fundamental importance to the progression of sodium-based batteries to be fully realized and be implemented over existing Li-ion based batteries.