The invention discloses an extraction of high activity milk thistle oil and a preparation method of a microcapsule of high activity milk thistle oil, and belongs to the technical field of biological processing. The preparation method comprises following steps: taking milk thistle seeds as the raw material, grinding milk thistle seeds, extracting milk thistle seeds by a mixed solvent composed of petroleum ether and anhydrous ethanol under the assistance of ultrasonic waves, carrying out centrifugal separation, vacuum concentration, and drying to prepare the high activity milk thistle oil; taking the milk thistle oil as the core material, carrying out emulsification by using an emulsifier glycerol stearate, taking soy isolate protein and Arabic gum as the wall material, and performing dissolving, homogenizing, re-agglomerating, centrifuging, and freeze-drying to obtain the milk thistle oil microcapsule. Under the assistance of ultrasonic waves, a mixed solvent is used to extract milk thistle seeds, the extraction time is short, the activity of the oil is obviously enhanced; the air in the microcapsule is expelled, unsaturated fatty acids in the oil are protected, the stability is improved, and the shelf life is prolonged. Moreover, the microcapsule has the advantages of good flowing property and good brewing property and is convenient to use, the product forms are enriched, andapplication range of the milk thistle oil is enlarged.