Abstract Aptamers as the recognition element of the stochastic nanopore sensors have been under intense investigation. This paper reviews recent research advances in aptamer‐based nanopore sensing techniques, including the classification and selection of nanopores (biological nanopores, solid‐state nanopores, and nanopipettes), different strategies of aptamer‐based nanopore sensing, and their values and outlook for applications in areas such as environmental analysis, precision diagnosis, pharmaceutical industry, and security. Furthermore, the single‐molecule nanopore sensors have been applied to reveal the aptamer‐target interactions, such as recognition orientation, binding sites, and conformational heterogeneity dissociation kinetics at the single‐molecule level. In this review, recent research efforts to develop aptamer‐based single‐molecule nanopore sensors with high selectivity and sensitivity are highlighted, and some perspectives are drawn.