Molecular biology was the science that expounded the phenomena and nature of biological life at the level of biological macromolecules such as nucleic acids, proteins, liposomes and so on, and its development has provided new techniques and methods for the study of Chinese medicinal resources. Gastrodia elata was an important traditional Chinese medicine and belonged to the homology of food and medicine. At present, the research on the molecular biology of Gastrodia elata was gradually deepening. In order to systematically expound the progress of the basic molecular research of Gastrodia elata, this paper summarized the latest research progress on the molecular biology of Gastrodia elata in the past more than ten years, mainly including Gastrodia elata molecular marker technology, functional genes, transcriptomics, genomics and so on. It was expected to provide a theoretical basis for the research on the genetic diversity, identification of germplasm resources, molecular breeding and cultivation management of Gastrodia elata.