The phase behavior as well as the microstructures of the cationic gemini surfactant and anionic conventional surfactant aqueous two-phase system (ASTP) have been studied. The ASTP formation can be attributed to the coexistence of different kinds of aggregates in the upper and lower phases. The effects of temperature, shearing, surfactant concentration and mixing molar ratio on the phase separation of the ASTP-forming systems are systematically investigated. The ASTP can be destroyed by applying shear and increasing temperature. In this process, the lamellar structures (flat bilayers) in the ASTP are transformed into vesicles. Variation of surfactant structure also affects the phase behavior and the aggregates transformation. Appropriate molecular packing is crucial for the formation of ASTP.