The structure of Na2O-GeO2 glasses has been investigated, using molecular dynamics (MD) simulations based on an empirical three-body interaction model. A multi-body potential function with two energy minima in the angular term for a given three-atom unit was introduced to permit a transformation between different coordination states, such as 4- and 6-fold coordinated Ge sites. Parameters in the potential function were optimized with a non-linear least-squares (NLS) method. The optimal parameter set obtained with a Na4Ge9O20 crystal was employed for the structural models of pure GeO2 and 2Na2O·9GeO2 glasses. In the model for the binary glass, however, a number of 5-fold coordinated Ge, non-bridging O and 3-fold coordinated O formed. Another binary model free from 5-fold Ge was prepared using a simple scheme in which no three-body interaction was applied to the structural units containing 5-fold coordinated Ge. All the structural models produced showed good agreement with the experiments, including vibrational spectra and radial distribution functions (RDFs). No significant difference between the experimental observables of the two binary glass models was revealed, except for the coordination environment of Ge. This is because 5- and 6-fold Ge do not occur in a discrete arrangement through a corner-sharing of GeO4, e.g. GeO5,6-GeO4-GeO5,6, but in a dense configuration, e.g. as edge-sharing GeO5,6-GeO5,6, forming smaller rings than those in pure GeO2 glass.