The influence of super-Gaussian velocity distributions on the ion feature of Thomson scattering off two-ion plasmas is studied. The analytical solution to the dispersion equation shows that although both the frequencies of the two (fast and slow) ion-acoustic waves increase with the index of the super-Gaussian, the slow wave is more weakly dependent on the index due to the screening of the light ions. In the case that plasma can sustain two lightly damped ion-acoustic waves, the inferred plasma parameters such as electron temperature and plasma temperature ratio may suffer some errors without consideration of super-Gaussian electron velocity distributions. Since the relative intensity between the resonant peaks of the fast and slow waves is sensitive to the super-Gaussian index, the super-Gaussian velocity distributions may be measurable with Thomson scattering off laser-heated two species ion plasmas.