Using a transient hot-wire method, the thermal conductivity of the CaO–SiO2–B2O3 mold flux system was measured. The effects of temperature, BO1.5 concentration and basicity on the thermal conductivity were considered, along with structural investigation by Raman spectroscopy. It was found that the addition of boron oxide caused both a decrement and increment of thermal conductivity, depending on the basicity. These conflicting effects on thermal conductivity were considered to be caused by the following two different behaviors in the oxide melts. Boron oxide is incorporated into silicate networks at a lower basicity, while it tends to form borate networks at higher CaO/SiO2 ratios. In the case of basicity dependency, thermal conductivity initially decreases or remains constant with increasing CaO/SiO2 ratio in regions of low basicity, but increases when the CaO/SiO2 ratio is higher than 1.15. Due to the incorporated state of boron oxide in silicate networks at low basicity, the thermal conductivity is likely to be predominantly affected by the silicate networks. However, at a relatively high CaO/SiO2 ratio, an increase in chain-type metaborate was observed through Raman spectroscopy; this structural change in borate being responsible for the increment in thermal conductivity with higher basicity. Finally, the apparent activation energy of thermal conductivity was calculated, and was found to be reduced by the addition of boron oxide.