The aggregation behaviors of a Gemini surfactant [C12H25(CH3)(2)N+(CH2)(2)N+(CH3)(2)C12H25]Br-2(-) (12-2-12) in two protic ionic liquids (PILs), propylammonium nitrate (PAN) and butylammonium nitrate (BAN), were investigated by means of several experimental techniques including small and wide-angle X-ray scattering, the polarized optical microscopy and the rheological measurement. Compared to those in ethylammonium nitrate (EAN), the minor structural changes with only one or two methylene units (-CH2-) increase in cationic chain length of PIL, result in a dramatic phase transition of formed aggregates. The critical micellization concentration was increased in PAN, while no micelle formation was detected in BAN. A normal hexagonal phase was observed in the 12-2-12/PAN system, while the normal hexagonal, bicontinuous cubic, and lamellar phases were mapped in the 12-2-12/BAN system. Such aggregation behavior changes can be ascribed to the weaker solvophobic interactions of 12-2-12 in PAN and BAN. The unique molecular structure of 12-2-12 is also an important factor to highlight such a dramatic phase transition due to the PIL structure change.