The hypothesis posits that the synergistic combination of morpholinium cations and specific aromatic counterions in surface-active ionic liquids (SAILs) will markedly impact the micellization behavior and aggregation properties of these SAILs, potentially resulting in heightened surface activity and distinctive structural features. Two SAILs, N-dodecyl-N-methylmorpholinium benzenesulfonate ([C12mmor][BS]) and N-dodecyl-N-methylmorpholinium β-naphthalenesulfonate ([C12mmor][β-Nsa]), were synthesized through quaternization and metathesis reactions. Surface tension (ST) and electrical conductivity measurements were employed to ascertain the critical micelle concentration (CMC), micellization behavior, and various thermodynamic and interfacial parameters of the SAILs. Subsequently, their structural properties were examined using a small-angle neutron scattering (SANS) instrument at multiple concentrations to identify distinctive features in the micelle structures. The intermolecular interactions were studied using density functional theory (DFT) calculations. The findings reveal substantial influences of aromatic anions on micellization behavior and aggregation properties of SAILs compared with conventional surfactants and imidazolium-based SAILs, with discernible structural characteristics elucidated through SANS where a formation of prolate ellipsoidal micelles of different size were observed. This research underscores the potential applications of these innovative ionic liquids in drug development and delivery, emphasizing the crucial role of counterion and headgroup selection in tailoring their properties for specific purposes.