The invention provides a seaweed ferment probiotic microcapsule and a preparation method thereof. The microcapsule comprises a microcapsule wall, a microcapsule core material and a core material carrier, wherein the microcapsule wall is prepared from sodium alginate, chitosan and calcium chloride, the microcapsule core material is prepared from seaweed ferment and probiotic, and the core materialcarrier is corn starch. The seaweed ferment probiotic microcapsule of the invention can effectively block the influence of gastric acid and the like on the viable bacteria number and activity of the probiotic, so that the seaweed ferment and probiotic act on the intestinal micro-ecological environment together, and the unique biological effect is achieved. The preparation method is simple in process, is relatively low in cost, and is easy to store and transport. Compared with other probiotic products, the microcapsule has the advantages of good film-forming property, strong stability, high probiotic survival rate, good slow release efficiency and the like, is suitable for embedding and controllable release of various probiotics, and has good application prospects.