Nucleic acid is the major physical basis of genetic information for storage, replication and transmission. Realizing accurate and sensitive detection of nucleic acid plays an important role for DNA lesion analysis, gene therapy, mutation analysis, bacterial infection, R&D of drugs, clinical diagnosis and so on. DNA sensing has a wide range of applications, such as environment, biomedicine, pharmaceutics, food, forensic medicine and other fields. Traditional methods mainly include optics, piezoelectric deoxyribonucleic acid sensing, electrochemical deoxyribonucleic acid sensing and surface plasmon resonance. With the rapid developments of genetic engineering technology, many new interdiscipline analytical tools in the field of life science have attracted widespread attentions. As a high-sensitive single molecule detection technology, nanopore sensing technology has got a fast development pace. Nanopores, with its unique physical and electrical properties, detect bio-molecules rapidly without labeling or amplification, and have been proven to be very useful. The progress of nanoporebased sensing technology for nucleic acid detection about DNA sequencing, DNA methylation detection, DNA lesion detection, Protein-DNA interaction, hevay metal ion detection, RNA and virus detection are reviewed.