Biological ion channels featuring asymmetries in structure, composition, and charge distribution have superior controllable ion transport properties, such as ion selectivity, ion gating, and ion rectification, by which life executes diverse activities, including signal transduction, cell motility, and mass and energy transfer. Inspired by this, researchers have never stopped pursuing artificial ion channels that can achieve comparable functions. Despite successful explorations in many fields, current homogeneous nanochannels, however, have not yet offered sufficient rewards comparable to those of their natural counterparts. However, hierarchically engineered heterogeneous nanochannels have gradually come onto the stage because of their excellent ion selectivity, permeability, and rectification properties and thus have been shining brilliantly in fields such as selective ion transport, energy conversion, biomolecular separation, and detection. In this article, we briefly review the recent advances of hierarchically engineered nanochannel systems in terms of pore-on-pore and pore-in-pore structures, with an emphasis on promising applications, including ion-selective transport, osmotic energy harvesting, separation, and biosensing. Finally, current challenges and conceivable solutions are also discussed to advance the design and applications of hierarchical nanochannel systems.