First-principles molecular dynamics simulation (FPMD) has been applied to study the ionic structure and electronic properties of Na3AlF6 molten salt. The results show that the main forms of complex ion groups in molten salt are [AlF4](-), [AlF5](2-) and [AlF6](3-), with the proportion of 10%, 60% and 30%, respectively. The electron orbitals near Fermi level are mainly occupied by F-2p and hybridize with Al-3p orbitals, in which electrons are transferred from Al-3p orbitals to F-2p orbitals. The calculation results of Raman spectra on [AlF4](-), [AlF5](2-) and [AlF6](3-) are close to the experimental values, indicating FPMD is applicable to similar molten salt systems.