The invention specifically relates to a bifidobacterium microcapsule and a preparing method thereof. The bifidobacterium is obligatorily anaerobic and very sensitive to oxygen, PH, temperature, humidity, and other adverse external environment, thereby being very hard to remain activity during production, storage and transport; besides, if taken orally in a form of dry bifidobacterium powder, the bifidobacterium cannot tolerate low-pH value gastric acid, bile salt, and other environments, so a purpose that massive survived bifidobacteria arrive at an intestinal tract and colonise on the intestinal mucosa is hard to be guaranteed. The preparing method disclosed by the invention comprises the following steps of: adding freeze-dried bifidobacterium powder into a sodium alginate solution and then mixing in soybean oil, emulsifying the mixed solution and standing; centrifugally collecting micro-capsules; and drying the micro-capsules by using a vacuum freeze-drying technology. The bifidobacterium microcapsule disclosed by the invention has the advantages of gastric acid resistance, bile salt resistance and entericsolubility, high survival rate of bifidobacterium, simple preparation method, strong practicality, convenience for industrial production, and excellent storage stability and solves the problem of short storage period of probiotics preparations.