The ATR-FTIR spectra of aqueous LiClO4, NaClO4, and Mg(ClO4)2 solutions with ClO4− concentrations ranging from 0 to 3.00 mol dm−3 were obtained. After subtracting the spectra of pure water, positive peaks on the high wavenumber side and negative peaks on the low wavenumber side of the O–H stretching bands are observed in the difference spectra. The positive peaks appear constantly at about 3580 cm−1 independent of cation, which are assigned to the water molecules weakly hydrogen-bonded with ClO4−. However, the negative peaks appear at 3203, 3196, and 3254 cm−1 for LiClO4, NaClO4, and Mg(ClO4)2 solutions, respectively, and the peak areas show significant difference with increasing the concentration of perchlorate anions and are dependent on cations. The negative peaks are attributed to the “structure breaking” effect of perchlorate ions on the hydrogen bond network of water, which is in agreement with Raman spectroscopic studies. Besides the “structure breaking” effect of ClO4− on destroying the strong hydrogen bonds of the water molecules with fully hydrogen-bonded five-molecule tetrahedral nearest neighbor structure, the difference of the negative peaks are the results of the different “structure making” effect of the three cations, which is consistent with the ability of the polarization and hydration, in the order of Na+ < Li+ ≪ Mg2+. The overall shifting of the v3 band of perchlorate ions towards low wavenumber with increasing the concentration of perchlorates is attributed to the presence of solvent separated ion pairs, i.e., M⋯(H2O)n⋯ClO4−. The symmetric stretching vibration (v1) of perchlorate ions, which is an infrared inactive mode for free perchlorate ions, shows a weak band at ∼930 cm−1 in a wide concentration range of the three systems. The appearance of the weak band is considered as the perturbation of the ZnSe/water interface on perchlorate ions.