Prime Editor (PE) is an innovative gene editing tool based on the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas) system, which has revolutionized multiple fields, including genetics, medicine, and agriculture. Emerging as a successor to Base Editor (BE), PE has gained worldwide attention due to its ability to introduce base substitutions, insertions, and deletions without causing double-strand DNA breaks, which significantly reduces the risk of off-target effect and unwanted genetic change. Notwithstanding its immense potential, researchers need to address PE's long encoding sequence and low editing efficiency for its maximal applications. Researchers have been working relentlessly to explore and enhance the editing efficiency and safety of PE by modifying its protein scaffold, optimizing the guide RNA design, and identifying cellular factors that influence its activity. Improved PE variants have been developed with enhanced accuracy and efficiency as well as decreased off-target effect when compared with their initial versions, demonstrating their potential in gene editing-related applications. Several strategies have been investigated to enhance PE performance, including: ① Modifying the structure of PE proteins to increase their efficiency, specificity, and binding affinity, thereby significantly improving their editing activity. ② Optimizing the design of pegRNAs, such as modifying the length, composition, or structure, that can boost PE's editing efficiency. ③ Identifying and manipulating cellular factors, such as proteins and RNAs, that bear functional relationships with the PE system, thus greatly enhancing its gene editing capabilities. ④ Developing automated design tools to facilitate the customization of the PE system for specific applications, vastly improving its practicality in research and clinical settings. Finally, this article summarizes the applications of PE in engineering animals and plants and developing gene therapy. Despite much room for further improvement in PE, significant advances have been made in improving its editing efficiency and safety. The rapid development of Cas9 and BE for treating genetic diseases stands as compelling testimony to the potential of PE in advancing gene editing technologies and applications. With continued research and development, PE holds great promise for improving human health and well-being.