Abstract: As a most important biomedical technology, DNA sequencing, especially single molecule sequencing, has become a research focus not only in biology but also in engineering and physics. It combines nanofabrication, optoelectronics, microfluidics, and molecular biology technologies together to develop our capability to detect the activities of single nucleotides. In this review, the nanostructure devices for single molecule sequencing are summarized. The principle and structure of zero-mode waveguides and nanopore devices are described in detail, as well as the challenges of single-molecule sequencing.