The effect of Na2O and temperature on the thermal conductivity of the Na2O-B2O3 binary system has been measured using the hot-wire method to examine the relationship between the thermal conductivity and structure in high-temperature melts. The thermal conductivity of the binary melt is measured from 1173 to 1473 K in the fully liquid state. The thermal conductivity slightly increases with Na2O content up to 20 wt%. Above 20 wt% Na2O, the thermal conductivity decreases with increasing Na2O. The network structure of molten glass was analyzed using Fourier transform infrared (FTIR), Raman spectroscopy, and XPS. The FTIR analysis shows that 3-D complex borate structures, such as tri-, tetra-, and pentaborate are made by [BO4] tetrahedral units interconnected with 2-D structure boroxol rings in the low Na2O region. Above 20 wt% Na2O content, nonbridged oxygen in [BO2O-] units and diborate groups increase with increase in Na2O. The same tendency is shown by the Raman spectroscopy and XPS analyses. The Raman analysis shows that boroxol rings disappeared with large [BO4] groups, such as tri-, tetra-, and pentaborate structures, which increase at low Na2O content. Isolated diborate groups and nonbridged oxygen in [BO2O-] units increase at high Na2O content. It can be inferred that single structure units, such as isolated diborate groups, interfere with conduction. The XPS analysis results show that free oxygen produced by the interconnection of Na2O in the borate structure does not cause significant changes to O2- in the low Na2O region, but increases the O-o and decreases the O-. Above 20 wt% Na2O, O- slightly increases and O-o shows a decreasing trend.