In this study, we employ molecular dynamics simulations to investigate how the cation's alkyl chain length, and thus the cation hydrophobicity, affects the solvation structure of Ubiquitin by ionic liquids. Specifically, we compare the interactions of the protein with two cations: 1-butyl-3-methylimidazolium ([BMIM]⁺) and 1-ethyl-3-methylimidazolium ([EMIM]⁺). Our analysis focuses on the differences in how these ILs interact with the protein surface at varying concentrations, emphasizing the role of increased cation hydrophobicity in driving water exclusion, promoting solvent aggregation, and influencing preferential solvation. We show that the increased hydrophobicity of [BMIM]⁺ enhances its accumulation near the protein surface, especially in systems with strongly interacting anions like [DCA]⁻ and