Abstract: The cultivation of high quality tobacco varieties is an important aspect of tobacco breeding. With the development of tobacco genomics, tobacco researchers have made a series of important original research achievements in dissecting complex traits in tobacco, such as quality, providing numerous genetic resources for tobacco breeding. This review aims to summarize the progress of gene discovery and functional analysis of polyphenol metabolism, glandular trichome and nicotine biosynthesis in tobacco. It is considered that exploiting candidate genes by using multi-omics technology, conducting functional identification by gene editing technology and synthetic biology technology, are important development directions for future research. Moreover, it is pointed out that further and more depth research on germplasm resources, strengthening the exploration and research of functional genes, and making breakthroughs in new technologies, are necessary to resolve the problems and shortcomings in tobacco quality breeding.