Amino acid ionic liquid - H2O mixtures have been widely used in recent years. Molecular dynamics (MD) simulations were used to investigate the nanostructures and interactions of two kinds of amino acid ionic liquids, 3–propyl-tributyl-alanine phosphate ([aP4443][Gly]) and 3-propyl-tributyl-alanine phosphate ([aP4443][Ala]) at different water molar fractions (xw = 0 – 0.95). Analysis of volume property showed that there were hydrogen (H) bonds between water molecules and ionic liquids, and the nanostructures of the mixture changed dramatically at about xw = 0.7. MD simulations showed that with the increase of water concentration, the structural correlations between anion - cation, cation - water, anion - water and water - water weakened and the relaxation time of H bonds decreased. The water molecule oxygen atoms competed with the anion carboxyl group to form H bonds with the amino group of the cation. Strong H bonds were also observed between anions and water molecules. Water molecules had different aggregation states at different water concentrations. In the concentrated ionic liquids – H2O mixtures, the anions and cations formed a stable network structure, and the H bonds in the system mainly consisted of H bonds between anions - cations. When 0.7 > xw ≥ 0.5, the H bonds between anion - water were the main component of H bonds in the system. When xw ≥ 0.7, the number of water - water H bonds in the mixture increased rapidly, the diffusion coefficients of the anions and cations increased exponentially, and the stable network of the ionic liquids was destroyed. The ion aggregation region was gradually divided by water molecules. When xw ≥ 0.9, water molecules were interconnected to form a large water network structure, and ionic liquids were gradually dissolved in the water molecules.