Abstract: Due to the rapid development of gene sequencing technology, microbiome research, and bioinformatics, the research on natural products from human microbiota has made significant progress in recent years. With more in-depth research, it has been found that the bioactive natural products produced by human microorganisms may frequently participate in the interactions between host-microbe and inter-human microbiota, with direct or indirect influence on human health. Many of these molecules exhibit the potential to become drug candidates or biomarkers for disease diagnosis/treatment. Therefore, researches on natural products from human microbiota may not only expand the source of bioactive natural products for drug discovery, but also be helpful in disease diagnosis and improving human health. This review summarizes three types of strategies for natural product discovery from human microbiota, with particular introduction to the discovery methods of a number of representative molecules as well as their structure and bioactivity diversity, so as to provide reference for further in-depth research in related fields.