An innovative gene editing system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has significantly revolutionized agriculture by improving the quality of crops and sustaining environment. It has become the most powerful tool for crop improvement due to its flexibility. CRISPR adapted the natural bacterial and archaea defense mechanism against invading viruses or other foreign DNA into a genome engineering tool that has remarkable crop breeding progress by virtue of its precision in specific gene editing. This study outlines the current application of CRISPR/Cas9 technology in crop yield, quality, disease resistance and environmental stress. In plants, CRISPR/Cas9-based gene-editing consists of the selection of specific target sites, designing and synthesis of single guide (sgRNA), delivery of transformation carrier or ribonucleoprotein (RNP) in plant cells, transformation, and regeneration of gene-edited plants. At present, the plant CRISPR/Cas9 and its derived system have shown several genome-editing activity, like gene editing, homology-directed repair (HDR), and transient gene silencing or transcriptional repression as well. Furthermore, simultaneous editing on multiple genes has contributed to pathway-level plant biotechnology researches that widely expand genome engineering of agronomic traits, and its adoptability. In addition, the challenge in the future application is also discussed. The CRISPR genome editing technology is not only equivalent to traditional breeding technique but actually much more controlled and faster.