Nanopores and nanochannels are ubiquitous, from biological systems to various artificial materials. Taking advantage of size confinement and tailoring the interior components, numerous functions can be achieved such as selectivity, gating, rectification, and so on, which result from diverse interactions between ion/molecule and nanopore/nanochannel. In this Perspective, on account of the summarized critical principles, namely size/shape, wettability, charge, recognition, and other interactions during ion/molecule transportation in nanopores and nanochannels, we introduce four main sections of applications: selective transportation in separation, controllable gating systems, energy conversion devices, and sensors. In addition, some typical challenges and possible future research endeavors in the related fields will also be discussed.