The invention discloses a probiotic liquid preparation based on a double-emulsion structure and a preparation method thereof. The method comprises the following steps that S1, a probiotic bacterium suspension, a thickener and an intestinal tract auxiliary release material (namely a material capable of assisting in the release of probiotics in an intestinal tract) are mixed, and induction is carried out with bivalent salt ions to form a gel-like inner water phase W1; S2, an oil-soluble emulsifier is dissolved in edible oil to form an oil phase O, and the oil phase O and the inner water phase W1are subjected to high-speed shearing and mixing so as to obtain a water-in-oil type primary emulsion W1/O; and S3, a suspension of colloidal particles is served as an outer water phase W2, the outerwater phase W2 is added into the primary emulsion W1/O, and intermediate-speed shearing and mixing are carried out so as to obtain the probiotic emulsion preparation based on the W1/O/W2 type double-emulsion structure. According to the probiotic liquid preparation and the preparation method thereof, protective embedding is carried out on probiotics by adopting a Pickering double-emulsion system, so that the probiotic effect is fully guaranteed, meanwhile, the probiotics can be prevented from being damaged by oxygen and the environment of a gastrointestinal tract, and therefore the action of gastric acid and cholate can be resisted, in addition, colonization can be better carried out in the intestinal tract, and a wide application prospect is achieved.