Understanding the aggregation selectivity of peptide fragments of full‐length proteins in aqueous solutions with ionic liquids (ILs) could facilitate the elucidation of the relationship between the IL‐protein interactions and structural behavior of intrinsically disordered proteins (IDPs) such as amyloid β protein following the addition of ILs. In the present study, we investigate structural changes in peptide fragment 1‐11 (Aβ1‐11) of amyloid β protein in aqueous solutions with two ILs including 1‐butyl‐3‐methylimidazolium thiocyanate ([bmim][SCN]) and ethylammonium nitrate (EAN) using optical spectroscopy. The addition of [bmim][SCN], which exhibits strong protein denaturant ability, induced the formation of an intermolecular β‐sheet structure (aggregation), while the addition of EAN, which has a weaker denaturant ability compared with [bmim][SCN], did not cause aggregation. Since the role of cations is related to the ability to mask the charged residues of Aβ1‐11, the aggregation selectivity of Aβ1‐11 depends on the anionic species and anions with high denaturation ability enhanced aggregation. Our results demonstrated that the structural change in peptide fragment in aqueous IL solutions could be used to evaluate the relationship between the IL‐protein interactions and aggregation selectivity in IDPs in aqueous IL solutions.