The system of clustered regularly interspaced short palindromic repeats(CRISPR) and CRISPR-associated endonucleases(Cas) have been widely used in gene editing, disease treatment, molecular diagnosis and chromosome imaging. On account of the programmable target recognition of CRISPR-Cas system and the specific targeting function toward RNA of type VI class II Cas proteins, CRISPR-Cas system has been deployed as RNA recognition and detection tools, exhibiting promising application potentials in the field of RNA detection and imaging. In this review, we summarize the latest research progresses as well as development prospects of CRISPR-Cas system in RNA diagnosis and live cell RNA imaging.