The invention discloses a functional drink containing natural gardenia jasminoides ellis extract and a preparation method of the functional drink. The functional drink comprises the following components in percentage by weight: 1*10<-4>-2*10<-2>% of natural gardenia jasminoides ellis extract, 1*10<-3>-9*10<-3>% of potassium sorbate and the balance of negative oxygen ion water. The produced finished product takes water as a carrier, contains 99.97% of purified water, is prepared into a popular drink (beverage) convenient to eat, is free of harmful additives, intermediate ingredients or drug ingredients, has a food-grade formula, and is equivalent with drinking water in the aspect of safety. In the preparation process, the natural gardenia jasminoides ellis extract is subjected to rupture of membranes, decomposed and recombined by adopting special processes and special-purpose equipment, so that the ratio and speed of the effective ingredients of the natural gardenia jasminoides ellis extract absorbed by the human body can be greatly increased, and the immunity of the intestines and stomach can be recovered quickly. The pain of most of people with dysfunction of the intestines and stomach can be quickly relieved or eliminated by utilizing the functional drink disclosed by the invention, and the sub-health of the intestines and stomach can be effectively conditioned by drinking the functional drink daily.