The invention discloses a preparation method, preparation system and application of triplet probiotics microcapsules. The preparation method comprises the following steps of preparing combined culturemediums, performing inoculating and culturing of bacteria species, preparing bacterial emulsion, preparing the microcapsules, and performing drying. Through adoption of the preparation method disclosed by the invention, the activity of probiotics is effectively protected, so that the situation that after entering intestinal tract, the probiotics can quickly breed is guaranteed, then the probiotics can be at an advantage state in microorganism competition, and an advantage microbial population is formed; the prepared microcapsules are uniform in size, not adhered to each other, and high in mechanical strength; the prepared microcapsules are high in gastric acid resistance, so that the probiotics can be protected to safely pass through the stomach environment, the microcapsules have entericsolubility and bile salt resistance, and the situation that enough quantity of the probiotics can reach the intestinal tract or settle in the intestinal tract to achieve beneficial effects, can be guaranteed; and the process steps for preparing the microcapsules are very simple, the preparation cycle is shorter, the production cost is greatly saved, and large-scale industrial production is facilitated.