The local structures of ternary alkaline-earth hexaborides (MB6, M = Ca0.5Sr0.5, Ca0.5Ba0.5 and Sr0.5Ba0.5) have been analysed using X-ray pair distribution function (PDF) analysis, Raman spectroscopy and transmission electron microscopy (TEM). The results show significant local deviations from the average cubic structure within the boron sub-lattice and support the conclusion that rapid synthesis processes lead to the formation of coherent nanodomains over length scales of about 10 nm. Reverse Monte Carlo fitting of the PDFs allows for quantification of the displacement disorder within the boron sub-lattice as a function of sample composition. Detailed Raman spectroscopy studies and high-resolution TEM support the models derived from X-ray scattering. The average magnitude of the static displacement disorder varies by sample composition and positively correlates with the cation radius ratios across the three compositions. The new models form a foundation for future computational and experimental studies aimed at understanding and predicting properties of hexaborides.