Room-temperature ionic liquids (RTILs) are used as hierarchically multifunctional components by employing them not only as templates and co-solvents for fabricating nanostructured materials but also proton conductors for electrochemical devices. RTIL/aluminum hydroxide (RTIL–Al) hybrids containing various nanometer-sized shapes, including 1D nanorods with hexagonal tips, straight and curved nanofibers, nanofibers embedded in a porous network, and 3D octahedral-, polyhedral-, and angular spherical shapes are synthesized via a one-pot ionothermal process. The structures or shapes of the RTIL–Al hybrids are related to the anionic moieties, alkyl chain length of the RTILs, and the humidity during fabrication. In particular, the introduction of water molecules into the interface led to 3D isotropic growth of the hybrids by influencing intermolecular interactions between the RTILs and the building blocks. The shapes of the nanohybrids fabricated from RTILs containing short alkyl chains were dependent on the types of anions and on the level of humidity. These results indicate that the cooperative interactions between RTILs and aluminum hydroxides induces emerging shape-controlled hybrids. The shape-controlled nanohybrids show enhanced electrochemical properties compared to those of a conventional hybrid prepared by mixing RTILs and aluminum hydroxides, exhibiting tenfold or higher proton conductivity under anhydrous condition and thermal stability as a result of the continuous proton conduction channel and the one-pot-assembled nanoconfinement. This method is expected to be a useful technique for controlling the diverse shapes of nanometer-sized crystalline inorganic materials for a variety of applications, such as fuel cells, solar cells, rechargeable batteries, and biosensors.