Lab-on-a-chip has been used widely in rapid, high-throughput and low-consumption analysis of samples in biochemistry. The ion concentration polarization (ICP) produced by ion-selective transport of nanochannels provides a novel solution for problems in ultra-low concentration sample detection, systems biology and desalination. This paper reviews the applications of ion transport based on the principle of ICP in micro-nanofluidic systems. First, the fundamental governing equations of ICP are described. Then, the applications of nano-electrokinetic ion enrichment and ion current rectification (ICR) are introduced. Nano-electrokinetic ion enrichment is used mainly in the fields of molecular enrichment, ultra-low concentration sample detection and seawater desalination. ICR is applied mainly to the sensitive detection of analytical substances such as proteins, nucleic acids and small molecules. The application of ion transport based on ICP principle is summarized and the possible directions worthy of further research are proposed.