In the 1960s, Hladky and Haydon have succeeded in detecting ionic flows across thin lipid membrane when adding small lipid-soluble molecules such as surface-active polypeptides to artificial membrane, which has laid the foundation for decoding single strand DNA when it crosses the nanopore under an applied electric field. In this paper, we will review several kinds of protein nanopores used in single molecular sequencing, such as α-hemolysin nanopore, MspA nanopore and membrane-adapted phi29 motor protein nanopore.