Angelica sinensis (Oliv.) Diels belongs to the Apiaceae family. The root of A. sinensis, is used in traditional Chinese medicine for its antioxidant and immune regulation properties. The main active compounds in A. sinensis include organic acids, phthalides and coumarins, and their biosynthetic pathways are the focus of international attention. A. sinensis is prone to early flowering and bolting, which negatively impacts production for several reasons, including germplasm degradation and quality instability in artificial cultivation. The identification of top-geoherbalism of A. sinensis has also become the focus of recent research, as it would allow selection for breeds with excellent medicinal quality and remarkable curative effects. Advances in sequencing technology and bioinformatic methodologies have enabled extensive molecular and genetic studies in A. sinensis. In this review, we summarize the latest molecular research advances related to A. sinensis, including biosynthetic pathways and regulation of active compounds, and molecular underpinnings of early bolting and flowering and top-geoherbalism. We discuss limitations of the current research and propose prospective topics in need of further exploration.