Using molecular dynamics simulations, we investigated effects of inorganic salts on the structure and dynamics of a short α,β-polypeptide, BBA5. The simulations showed that three model salts, NaI, NaF, and Na₂SO₃, have very different effects on the structure of the polypeptide. The addition of NaI to the aqueous solution caused denaturation and significantly weakened hydrogen bonds of the polypeptide. Na₂SO₃ strengthened the hydrophobic interactions and increased hydrogen bonding of the polypeptide. Preferred binding of Na⁺ to the backbone carbonyl groups of BBA5 occurred in the NaI solution, consistent with the weakened protein backbone hydrogen bonds, whereas Na⁺ is excluded more from the vicinity of the protein backbone in the Na₂SO₃ solution. This difference in Na⁺ binding correlates well with the different propensities of the counter ions approaching the protein surface: SO₃²⁻ is much more strongly expelled from the protein apolar surface than I⁻, and demonstrates the importance of cation–anion cooperativity in affecting protein structures. The binding of the two salts to and their effects on the hydration of the protein surface depends strongly on the polarity of the latter. However, both salts reduce the flexibility of the polypeptide and the fluctuation of its hydration layer. These simulations showed that the chaotropic NaI affects protein structure mainly through a direct binding of Na⁺ to the backbone and I⁻ to the protein surface. The main effect of Na₂SO₃ manifests in strengthening the hydrophobic interaction and consequently the hydrogen bonding of the protein, more likely through an “indirect” mechanism. In addition, the simulations showed that NaF has a similar effect as Na₂SO₃ (but weaker than the latter, consistent with their positions in the Hofmeister series).