The controllable ion transport is the basis of most physiological activities, such as the transmission of neural signals, the perception of external stimuli, etc. The key to realize the controllable ion transport is the various protein ion channels in life system. Inspiring researchers endeavor to develop artificial ion channels to subtly tune the ion transportation. Among the developed ion channels, hydrogel-based system exhibits the advantages of high ion selectivity and high ion conductance due to its three-dimensional(3D) charged networks induced space charges and 3D interconnection channels. As hydrogel-based ion channels hold the biocompatibility, deformability, and stable ion storage properties, it has been the focus in intelligence ion transport field and shows great potential in ion electronic circuits, medical health, energy conversion and storage, resources, and environment. To summarize the latest development of the hydrogel-based ion channels, we firstly overview on the construction methods of hydrogel-based intelligent ion channels. Thereafter, the ion transport mechanisms in the hydrogel-based ion channels are summarized, and the applications of such ion channels are categorized. At last, we discuss the existed issues and give the perspective on future development of hydrogel-based ion channels.