It remains a challenge to establish structural models of multicomponent oxide glass systems. In this study, we have investigated 68.3SiO2–16.1B2O3–4.2Al2O3–11.4Na2O glass and melt structures by ab initio molecular dynamics (AIMD) simulations. The atomic configurations obtained from AIMD simulations were validated against 17O solid‐state NMR spectrum under 24.0 T and neutron diffraction data, and excellent agreement was achieved. The bond lengths, angles, and coordination geometries were statistically analyzed for each atomic species. Here we particularly address the role of minor atomic species such as five‐coordinate Si (SiV) and Al (AlV). The SiV–O bond lengths and O–SiV–O angle distribution in the glass indicated 1.718 Å and three peaks at 90°, 120°, and 175°, which are assigned to a coordination geometry of the trigonal bipyramidal structure. Ring statistic analysis revealed that SiV and AlV were found to preferentially contribute to the formation of small ring sizes.