Microorganisms have consistently been a crucial source for researchers to explore and develop new natural products. Currently, research methods involving gene editing tools for the discovery, biosynthesis, and metabolic engineering of natural products have garnered broad attention in this field. However, traditional methods for gene editing usually rely on the recombination ability of the host or introduced proteins. It’s difficult to establish a general platform for all bacteria mainly because of their complicated genetic background. This genetic diversity often causes laborious experimental operations with low efficiency. The CRISPR/Cas9 gene editing system, with its unique and flexible targeting advantages, overcomes common limitations such as sequence homology or site constraint in other gene editing methods and thus is more likely to function in diverse bacteria species. This simplifies experimental procedures, enhances work efficiency, and promotes the development of natural product research. This article introduces the applications of the CRISPR/Cas9 system for the discovery, biosynthesis, and metabolic engineering of natural products in microorganisms. It covers the development of the CRISPR/Cas9 system, cloning and genetic editing of natural product biosynthetic gene clusters, structural derivatization and metabolic engineering of natural products, and the activation of silenced natural product biosynthetic gene clusters. These aspects highlight the advantages of the CRISPR/Cas9 system in the research of natural products with microorganisms. Finally, solutions are proposed for addressing challenges that the CRISPR/Cas9 system currently faces in overcoming low recombination efficiency and host adaptability issues. Especially the CRISPR/Cas12a system which has broadened applications of the CRISRP/Cas9 system by preferring different PAM sites. In addition to functions that CRISPR/Cas9 system has realized, its potent multiple targeting ability further enhances the efficiency of target editing. It is believed that with the development of synthetic biology and information technology, an increasing number of genetic manipulation tools and methods related to the CRISPR/Cas9 system will be developed, continually driving progress in the research of natural products.