The invention provides a Probiotic microcapsule and a preparation method thereof, relating to the technical field of Probiotic products. The method includes the following steps: (a) preparing a capsule core containing Probiotics: mixing the capsule core materials including Probiotic powder, microcrystalline cellulose and starch, then adding a hydroxypropyl methylcellulose solution thereinto, while mixing evenly, making the obtained mixture materials into spherical particulate capsule cores by the extrusion spherization method; (b) coating by atomization: coating the microcapsule cores with a coating material solution in a single layer or multiple layers by atomization, getting core-shell microcapsules. The Probiotic microcapsules prepared by the present invention have a large encapsulation, uniform microcapsule particles, controllable particle size, storage-resistance, targetability to intestinal tracts, resistance to gastric acids and high temperature stability.