Fluorine plays an important role in glass, ceramic, metallurgy, welding, etc. Few studies have investigated the role of fluorine in the molten aluminium-silicate slags. Herein, classical molecular dynamics (MD) simulation combined Raman spectroscopy technique was employed to investigate the influence of Al2O3/SiO2 (A/S) ratio on short- and medium-range order structures of molten CaO-SiO2-Al2O3-Na2O-F (CSANF) slags. Then, partial least squares (PLS) modeling was used to explore the latent relationship between the microstructure and diffusion coefficient of ions was further analyzed. The results show that in the molten CSANF slags, the F− mainly coordinates with Na+ and Ca2+, and the coordination of Ca2+ with F− is most stable. The volatilization of fluoride in the molten CSANF system can be prevented by increasing Ca2+, reducing Na+, and reducing the polymerization of Si-O network. Collectively, this study provided a comprehensive understanding of the microstructure and volatilization mechanism of fluorine in silicate melt.