Sodium-ion batteries (SIBs) are gaining much attentions due to their potentials to achieve large scale energy storage coupled with relatively low cost. However, typically used organic electrolytes with high flammability and poor thermal stability have impeded further developments of SIBs in large-scale energy storage. Ionic liquids (ILs), featuring excellent thermal stability, non-flammability and wide electrochemical window have been promising alternative electrolytes for SIBs. Herein, rechargeable Na/Na3V2(PO4)3 cells with NaPF6-incorporated 1-butyl-3-methylimidazolium bis (trifluoromethanesulfonyl) imide BMITFSI IL electrolyte are demonstrated to reduce the flammability of the electrolyte and improve the safety of cells. Besides, the electrochemical performances of SIBs are enhanced by forming a stable solid-electrolyte interphase (SEI) layer on the cathode. The optimized Na/Na3V2(PO4)3 cells with the IL electrolyte exhibit high initial discharge specific capacity of 107.2 mA h/g and good cycling performance, which is superior to that using carbonate organic electrolyte. Remarkably, the formation mechanism of the SEI layer on the Na3V2(PO4)3 cathode in NaPF6/BMITFSI IL electrolyte for SIBs is put forward in this work according to density functional theory (DFT) calculations and confirmed by Raman, energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and fourier-transform infrared spectra (FTIR) tests, where NaOH, Na2SO4, Na2S2O7 and NaF are assigned as the major inorganic components of SEI. These results show that NaPF6/BMITFSI is a promising electrolyte to improve the safety and electrochemical performances of SIBs.