Molecular dynamics simulations were conducted to investigate the interactions of cysteine tripeptides with ions and water molecules in solutions of salts (MA, M = Li+ and Cs+, A = halide ions). The results revealed that as the anion size increases, cations aggregate more easily around the tripeptide, irrespective of capping. Radial distribution function (RDF) analysis showed direct interactions between F− and tricysteine, whereas Cl−, Br−, and I− exhibited indirect binding. Comparison between Li+ and Cs+ systems indicated that the smaller Li+ ions tend to distribute more around the tripeptide, engaging in direct interactions, whereas Cs+ ions interact indirectly, mediated by water molecules. Interaction energy analysis demonstrated that in lithium salt solutions, the total energy of anions with tricysteine decreased with anion size for both capped and uncapped systems. In cesium salt solutions, the anionic I− had the strongest interaction with cysteine tripeptides, and the cationic Cs+ interaction with tripeptides peaked in the CsI solution. The results highlight differences in ionic interactions depending on the anion-cation correlations of different salts.