As a fuel or energy carrier, hydrogen has been identified as a key way to decarbonize electricity, industry, transportation, and heating sectors. Hydrogen can be produced by a variety of methods, among which water electrolysis driven by renewable energy is sustainable and nearly carbon-free. To use hydrogen widely, storage and transportation over long distances are another key issue. Apart from storage at high pressure and low temperature, hydrogen can be stored in organic compounds via chemical bonding under relatively mild conditions. Efficient utilization of hydrogen includes hydrogen fuel cells as an alternative to internal combustion engines. From the above scenarios, catalysis and reaction media are the key factors for realizing hydrogen energy implementation. Ionic liquids (ILs) offer new opportunities due to their tunable functional groups, low vapor pressure, and stable structures as additives, solvents, and charge transfer materials. ILs are known to produce solid catalysts with controllable properties, decorate solid catalysts with modified electrons and geometric structures, and serve as electrolytes and hydrogen storage media. This review summarizes and recaps the recent progress in how ILs act as a cornerstone to support the production, storage, and utilization of hydrogen. Furthermore, critical challenges and future research directions of ILs in hydrogen energy applications are also outlined.