Materials featuring well‐defined nanoscale channels have demonstrated inherent advantages in the selective transport of gases, liquids, and ions, making them pivotal in applications such as molecular separation, catalysis and energy storage. A crucial challenge lies in the assembly of ordered nanochannel structures and the transformation of such microscopic ordered structures into macroscopic regular distributions to achieve performance improvements. Nanocomposites provide a promising solution by incorporating nanoscale material (e.g., filler) that significantly enhance macroscale properties of matrix (e.g., polymer). In this review, we spotlight nanocomposite membranes that leverage the confinement effects between filler and matrix to construct precise nanochannels and regulate the nanochannel distribution. We discussed the underlying design principles, channel architectures, and the manipulation strategies for integrating filler and polymers into functional membranes. Emphasis is placed on the fundamental mechanisms of mass transport, and the structure‐property‐performance relationships within the nanocomposite membranes towards molecular separation. This work aims to provide a comprehensive understanding of how these nanocomposite membranes can be further developed to meet the demands of industrial and environmental applications.