• Thermal conductivity of alkaline earth borate melts is investigated systematically for the first time using transient hot-wire method. • Thermal diffusivity is extrapolated from thermal conductivity, heat capacity and melt density, providing a new approach to thermal diffusivity measurement. • Short-range and intermediate-range order of alkaline earth borate structure is studied using high-resolution MAS-NMR, Raman spectroscopy and XPS for a precise and comprehensive insight into structure-conductivity relationship. • Compositional dependence of thermal conductivity is revealed with the discussion on “boron anomaly” phenomenon in alkaline earth borate melts. In this work, the thermal conductivity of alkaline earth borate melts was measured using hot-wire method from 1323 to 1623 K, and the thermal diffusivity was extrapolated from the thermal conductivity and heat capacity. The compositional dependence of thermophysical properties was interpreted according to the structure in short-range and intermediate-range order. Based on the Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and 11 B magic-angle spinning nuclear magnetic resonance (MAS-NMR) spectra, modifier cation with higher field strength prefers the formation of non-bridging oxygens (NBOs) for the charge compensation at high BO 1.5 / M O ratios. A lower amount of covalent bond and greater isolation of large borate groups lead to a lower thermal conductivity in calcium borate melt compared with strontium and barium borates. But the large size of Ba 2+ encounters difficulty in fitting around B [4] -O-B [4] linkages inside the overcrowded large borate groups when BO 1.5 /BaO = 2.5, promoting the formation of NBOs on the edge of borate groups for the charge compensation of modifier cations and leading to the decline in the thermal conductivity. Thermal conductivity plays a major role in regulating the thermal diffusivity at a given temperature since the compositional dependence of volumetric heat capacity is relatively weak compared with that of thermal conductivity.