In recent years, CRISPR/Cas9 system has rapidly become the most revolutionary gene editing tool in the field of medicine. It is the third-generation artificial endonuclease after Zinc-finger nucleases (ZFNs) and transcription activator-like effectors nucleases (TALENs), and is known as "gene scissors". CRISPR/Cas9 system relies on a synthetic single guided RNA (sg RNA) to direct Cas9 nuclease to cleave the target DNA sequence, so that it can complete genomic site editing. Based on the simplicity of design, rapid implementation, low cost and high efficiency, CRISPR/Cas9 system has been extensively studied in the fields of gene functional identification, antiviral therapy, anti-tumor therapy and immunotherapy. Although CRISPR/Cas9 system displays several obvious advantages, the risk of off-target would increase the therapeutic risks, hinder research and clinical application, which should not be ignored. How to reduce the off-target effects and increase mutation efficiency simultaneously as we use CRISPR/Cas9 gene editing technology? This will be an urgent problem for scientists to explore CRISPR/Cas9 technology and expand its clinical application in the future. Here, we briefly introduce the composition, mechanism and application of CRISPR/Cas9 system, and give a comprehensive introduction of the off-target effect which is widely concerned in this field at present, and summarize the optimization strategies to provide references for researchers.