The structure of aqueous mixtures of 1,1,1,3,3,3-hexafluoro-propane-2-ol (HFIP) has been investigated at an alcohol mole fraction (x HFIP ) of 0.1, 0.2, and 0.4 by molecular dynamics (MD) simulation. The simulated pair correlation functions were compared with those obtained by empirical potential structure refinement (EPSR) modelling combined with neutron diffraction with isotopic substitution experiment. It is demonstrated that microheterogeneities of HFIP and water clusters occur at x HFIP = 0.1 and 0.2 and that the tetrahedral-like structure of water is mostly disrupted at x HFIP = 0.4. The evolution of the microscopic structure of the water-water, alcohol-water, and alcohol-alcohol pairs with alcohol concentration is revealed in terms of pair correlation functions and discussed from the standpoint of hydrophilic and hydrophobic hydration.