The structure of ionic liquids (ILs) has an influence on their physiochemical properties, determining their performance as self-assembly media. In this study, we focus on the anion effect of aprotic ionic liquids (AILs). The aggregation behaviours of the cationic surfactant 1-hexadecyl-3-methylimidazolium bromide (C16mimBr) have been investigated in the imidazolium AILs with the 1-ethyl-3-methyl imidazolium cation and different anions, including nitrate, ethylsulfate, bis(trifluoromethylsulfonyl) imide and tetrafluoroborate. Surface adsorption parameters of C16mimBr were determined using surface tension measurements, and the critical micellization concentration values in AILs vary for their different cohesive energy. The micellar and lamellar lyotropic liquid crystal phases emerge with the increase of C16mimBr concentrations. The structure and properties of aggregates were determined using small angle X-ray scattering, polarized optical microscopy, rheology and differential scanning calorimetry. The anion effects of AILs on the phase behaviours and structure and properties of aggregates were analysed and discussed. The lamellar lyotropic liquid crystals have shown good conductivity, as confirmed by electrochemical impedance spectroscopy characterization. Our results enhance the understanding of the structure effect of ILs as self-assembly media and contribute to the design of tailorable solvents.