Heterogeneous nanochannel materials that endow new functionalities different to the intrinsic properties of two original nanoporous materials have wide potential applications in nanofluidics, energy conversion, and biosensors. Herein, we report novel, interesting hydrogel-composited nanochannel devices with regulatable ion rectification characteristics. The heterogeneous nanochannel devices were constructed by selectively coating the tip side, base side, or both sides of a single conical nanochannel membrane with thin agar hydrogel layers. The tunable ion current rectification of the nanochannels in the three different coating states was systematically demonstrated by current-voltage (I-V) curves. The asymmetric ionic transport property of the conical nanochannel was further strengthened in the tip-coating state and weakened in the base-coating state, whereas the conical nanochannel showed nearly symmetric ionic transport in the dual-coating state. Repeated experiments presented insight into the good stability and reversibility of the three coating states of the hydrogel-nanochannel-integrated systems. This work, as an example, may provide a new strategy to further design and develop multifunctional gel-nanochannel heterogeneous smart porous nanomaterials.