The invention provides high-purity geniposide as well as preparation and clinical application of preparations thereof. Gardenia is a dried and matured fruit of rubiaceae plant gardenia and has liver-protecting, chole-promoting, pressure-reducing, heat-clearing, cold-promoting and diarrhea-relieving functions and the like. The geniposide is a product which is obtained by refining the dried and matured fruit of the rubiaceae plant gardenia by virtue of a high-technology production process and is an iridoid glycoside compound. The geniposide is used for treating cardiovascular and cerebrovascular diseases, hepatic and biliary diseases, diabetes mellitus and the like. At present, a lot of methods for extracting the geniposide and gardenia pigment from the gardenia are reported in documents, but a plenty of problems exit, such as the product contains high impurity content so that the requirements of customers at home and abroad can not be satisfied, the production cost is high, the yield is low, the economic benefits are poor, the methods are not suitable for industrial production, and the like. According to the invention, the problems are solved. The high-purity geniposide is obtained by virtue of extraction and purification of gardenia and is prepared into proper preparations such as tablets, capsules, particles, injecta, powder injections, infusion solutions and the like to be applied to the clinic for treating cardiovascular and cerebrovascular diseases, hepatic and biliary diseases, diabetes mellitus and the like.