Molecular dynamics (MD) simulations have been used to study the effect of Na ions on the structure properties of CaO–Al2O3–Na2O slag. The short- and medium-range structures of CaO–Al2O3–Na2O in this study are consistent with existing data. Through the replacement of Ca2+ ions with Na+ ions in CaO–Al2O3–Na2O slag, the structure of the AlO4 tetrahedron is stabilized as the proportion of AlO4 tetrahedron in the melt increases and the average values of the O–Al–O bond angle are closer to those of an ideal tetrahedron. The changes in the melt structure show that Ca2+ ions mainly play a role in modifying the network, while Na+ ions mainly play a role in the charge compensation of the AlO4 tetrahedron; thus, as more Na+ ions replace Ca2+ ions added to the melt, the charge compensation ability in the melt is enhanced, and the network modification ability is weakened. Part of the weak non-bridge oxygen (NBO) structures in the form of Al–NBO–Ca are transformed to strong bridge oxygen (BO) structures in the form of Al–BO–Al, and the microstructure of the melt gradually becomes complicated, which provides a reasonable explanation for the mechanism for the increase of macroscopic viscosity in CaO–Al2O3–Na2O slag with high Al content.