The electrochemical properties of Na3V2(PO4)2F3 cathode utilized in the sodium ion battery are investigated, and the ion migration mechanisms are proposed as combined via the first principles calculations. Two different Na sites, namely, the Na(1) and Na(2) sites, could cause two sodium ions of Na3V2(PO4)2F3 to be extracted or inserted by a two-step electrochemical process accompanied by structural reorganization that could be responsible for the redox reaction of V(3+/4+). Because the calculated average voltage (V(avg)) of the second charging plateau is 4.04 V for the optimized system but 4.38 V for the unoptimized one, the reorganization of the cathode system can make a stable configuration and lower the extraction energy. Three designed pathways for sodium ions along the x, y, z directions in Na3V2(PO4)2F3, known as a 3D ions transport tunnel, have activation energies (Ea) of 0.449, 0.2, and 0.323 eV, respectively, by using DFT calculations, demonstrating the different feasibilities of the migration directions.