Ionic liquids have become one kind of the most promising solvents for self-assembly. The aggregation behaviours of various surfactants have been studied in numerous ionic liquids, especially the cationic and nonionic surfactants. In this work, we would explore the aggregation behaviours of sulfobetaine zwitterionic surfactants (SB3-n, n = 12, 14, 16) in the protic ionic liquid ethylammonium nitrate (EAN). The micellization behaviour was studied by surface tension measurement and the critical micellization concentrations are much larger than those in water. The micellar phase and hexagonal lyotropic liquid crystal phase are formed by SB3-12 and SB3-14 in EAN while an additional micellar cubic lyotropic liquid crystal phase is formed in the SB3-16/EAN system. The structure of aggregates was characterized by the small angle X-ray scattering while optical and viscoelastic properties by polarized optical microscopy and rheology. The alkyl chain length effect of SB3-n on aggregation behaviours was discussed and compared with those in the other surfactant/EAN systems. Our results would provide the thorough understanding on aggregation behaviours of sulfobetaine zwitterionic surfactants in EAN.