Abstract: Medicinal plants represent the oldest form of medicine and have been used in traditional medicine in many countries for thousands of years. Medicinal plants are critical natural resources that can isolate active metabolites or compounds with pharmacological significance for humans. The World Health Organization pointed out that up to 80% of the population in developing countries mainly relied on plant-derived medicines. The world's demand for herbal medicines has increased year by year and is expected to reach USD 5 trillion in 2050. It is an inevitable development trend to realize the large-scale production of medicinal plants and their derivatives. The rapid development of modern sequencing technology has promoted the research of medicinal plant genomics, research of genomics based on interdisciplinary and high-throughput data analysis of DNA and RNA, metabolomics and proteomics, and breakthroughs have been made in the researches of medicinal plants in fields of metabolic pathways/enzymes, metabolites, genes, gene networks, and protein-protein interactions. Combined with the relevant research work of the team, this article summarizes the latest research progress of medicinal plant genomics, involving the use of structural genomics and functional genomics to reveal the genome sequence information, inter-species evolution, changes of molecular compound dynamics, and synthesis of medicinal ingredients. In terms of the synthesis of medicinal ingredients, these data provide an essential theoretical basis for molecular-assisted breeding of necessary medicinal materials, genome editing, and understanding the molecular mechanism of the chemical diversity of active compounds. The phytochemical composition and potential health benefits of many medicinal materials have not yet been studied or need to be further investigated. The future of medicinal plants is full of unknowns, hopes, and even surprises. Due to the diversity of species, the complexity of environmental factors, and the global distribution of medicinal plants, it is imperative to strengthen research work in conjunction with genomics to develop new and improved medicinal plant varieties.