The invention discloses a preparation method and application of artemisinic acid magnetic imprinting microspheres. Artemisinic acid serves as a template molecule, artemisinin serves as an auxiliary template, a magnetic Fe3O4 nano particle serves as a carrier, 4-vinylpyridine serves as a functional monomer, a TRIM-DVB mixture serves as a cross-linking agent, a surface imprinting technology is adopted, and the artemisinic acid magnetic imprinting microspheres are prepared; the obtained molecularly imprinting polymer particles are uniform in size, large in specific area and high in imprinting efficiency, the maximum static apparent adsorption amount of the imprinting microspheres for artemisinic acid is high, the artemisinic acid magnetic imprinting microspheres serve as adsorbent, enriched adsorbent can be selected from artemisia annua linn extract efficiently, the adsorbent can be rapidly separated through a magnet, washing and elution are conducted with solvent, a target compound can be separated, the recovery rate of artemisinic acid is 96.7%, and the product purity obtained after removal of solvent is higher than 80%. A novel separation material and method are provided for separation and purity of the bio active substance, namely artemisinic acid, in the artemisia annua linn.