The Class 2 CRISPR-Cas system has the function of multiple gene editing and modification, which completes the interfere progress by single-effect proteins, including Cas9 and Cas12 system for editing double-stranded DNA, and Cas13 system for recognizing and cutting single-stranded RNA. In this article, we systematically summarize Class 2 CRISPR-Cas system’s structure and functional, the interference mechanism as nucleases, and the application of Class 2 CRISPR-Cas system in tumor model construction, drug resistance research, tumor immunotherapy, nucleic acid detection etc. Thus, this article will provide important reference information for developing new CRISPR-Cas tools in further clinical research.