Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) is a kind of genetic structure containing interval repeat sequences and is widespread in bacteria and archaea genome. CRISPR/CAS system mediated by RNA can provide bacteria with a specific immune protection mechanism to resist the invasion of the virus or phage. Through the transformation of CRISPR/CAS system Ⅱ, it has become another efficient technology for targeted gene modification after the zinc finger nuclease (ZFNs) and Tate nuclease (TALENs), which is of flexibility, efficiency, cheapness and easy-operating. At present, CRISPR/Cas technology has been applied to many organisms such as microorganism, mammalian cells, fruit flies, rice and some research achievements in genetic modification have been obtained. The structure, classification, molecular mechanism of genome editing, application prospect in industrial microorganism and problems of CRISPR/Cas system are reviewed in this paper.