Panax has a long history as a traditional Chinese medicine, and has many pharmacological activities such as tonifying, anti-inflammatory and anti-tumor. In addition, the use of ginseng is gradually shifting from traditional medicine to food. Saponins are the effective components of ginseng plants, but because of their low content and the growing environment of ginseng plants getting worse, it is difficult to meet the use requirements. The variety, cultivation, producing area, harvest time, and other factors of Panax are very important to the quality of Panax saponins. In addition, rare saponins with low natural abundance can be produced by deglycosylation or side chain modification through physical and chemical processing or biotransformation. Most importantly, compared with the prototype saponins, they show strong biological activity, which leads to the research and development of ginseng and rare ginsenoside-related nutritional health products and natural products being highly concerned. Therefore, this paper summarizes the latest progress in the structural diversity, transformation routes, processed products of Ginseng plants from different places and years, and synchronous detection methods of rare saponins with different transformation methods, to provide the reference for the rapid discovery, quality control, and further development and utilization of rare saponins products.