In the last years, glass research focused particular attention on transition metal oxide containing systems for semi-conductive applications, for instance glasses for solid-state devices and secondary batteries. In glass matrices, transition metal ions show multiple oxidation states that lead to peculiar structures and to highly complex systems, which produce interesting optical, electrical and magnetic properties. Computational methods have been largely employed as complementary tool to experimental techniques, in order to improve the knowledge on the materials and their performances. In this work, Molecular Dynamic (MD) simulations have been performed on a series of alkali vanado-phosphate glasses in order to gain deep comprehension of the glass structure. The short and medium range order of the V4+ and the V5+ sites in terms of coordination, pair distribution function, V–O–V linkages, bridging and non-bridging oxygen distributions were calculated and discussed. Finally, the comparison between MD and experimental results shows a very good agreement allowing the validation of the computational models and highlights the correlations between the structure and the conduction mechanism in these glasses. This allows enriching the know-how on these glass systems that result still ambiguous until now.