The segregation and phase sequence of semifluorinated cat-anionic surfactant membranes at different excess surface charges was investigated by freeze-fracture transmission electron microscope (FF-TEM), X-ray diffraction (XRD), and nuclear magnetic resonance (NMR). The thermal behavior of the membranes was evaluated by conductivity, rheology, and deuterium nuclear magnetic resonance ((2)H NMR). The experimental results show that the cat-anionic fluorinated surfactant mixtures can form faceted vesicles and punctured lamellar phase when there is excess surface charge. The cationic and anionic fluorinated surfactants are stiff in the membranes, like phospholipids in the frozen "crystalline" or "gel" phase. For the system with excess cationic surface charge, the gel-like faceted vesicles and punctured lamellae can transform into smooth-shaped vesicles at 65 °C. However, for the system with no excess charge or with excess anionic surface charge, no phase transformation occurs even at 90 °C. A model was established to demonstrate the mechanism of the formation and transition of the aggregates with different morphologies. The segregation-crystallization mechanism works well with other cosmotropic counterions from the Hofmeister series. The observations provide a better understanding of how to control the membrane morphology of the aqueous solutions of cat-anionic surfactant mixtures.