The invention discloses a double-coating enteric doxycycline microcapsule, comprising a core, an inner coating layer and an outer coating layer. The weight ratio of doxycycline to an auxiliary material to the inner coating layer to the outer coating layer is (10-30) to (20-30) to (15-25) to (5-10). A preparation method of the double-coating enteric doxycycline microcapsule includes: 1), performing weighing; 2), performing mixing: mixing doxycycline and the auxiliary material, performing extrusion granulating and drying, and performing screening to separate pellets; 3), preparing a first layer of coating: adding an inner coating material to the pellets to obtain coated granules; 4), preparing a second layer of coating: spraying an outer coating solution to the surface of the granules to obtain spherical microcapsule granules; 5), performing drying to obtain a microcapsule preparation product. The double-coating enteric doxycycline microcapsule and the preparation method thereof allow doxycycline to not dissolve in the stomach but dissolve stepwise in intestines, thus being released slowly and prolonging acting time of doxycycline, the process is simple, production is convenient, the cost is low, and the double-coating enteric doxycycline microcapsule is suitable for batch production.