Two morpholinium-based surface-active ionic liquids (SAILs) with aromatic counterions were synthesized, namely, n-dodecyl-n-methylmorpholinium salicylate [C12mmor][Sal] and n-dodecyl-n-methylmorpholinium 3-hydroxy-2-naphthoate [C12mmor][3-h-2-n], and explored their aggregation behavior in aqueous solutions systematically. Electrical conductivity, small-angle neutron scattering (SANS), surface tension (ST), and UV-vis spectroscopy measurements were employed to determine various thermodynamic, micellar, and interfacial parameters, like the degree of counterion binding (β), critical micelle concentration (CMC), minimum area per molecule (Amin), surface excess concentration (Γmax), standard Gibbs free energy of adsorption (ΔGad0), aggregation number (Nagg), standard Gibbs free energy of micellization (ΔGm0), standard enthalpy of micelle formation (ΔHm0), and the standard entropy of micellization (ΔSm0) in an aqueous solution. Incorporating the aromatic counterions favors significantly excellent micellization properties over conventional halogenated SAILs such as [C12mmor][Br]. SANS analysis revealed that upon changing the counterion from salicylate to 3-hydroxy-2-naphthoate, the structure changed from prolate ellipsoidal micelles to large unilamellar vesicles. Also, increasing the concentration in the case of [C12mmor][Sal] resulted in a lower aggregation number.