The invention relates to a biological preparation method of a Hypericum perforatum L extractive, providing a preparation method which can utilize medicinal material resources adequately, has simple process, is suitable for large-scale production and can prepare the Hypericum perforatum L extractive in accordance with or higher than international standards. The method comprises the following steps of: drying the Hypericum perforatum L firstly and smashing into Hypericum perforatum L powder, then weighing enzyme, adding warm water in the enzyme to dissolve the enzyme, activating enzyme solution by water bath, mixing the Hypericum perforatum L powder with water, performing water bath, soaking, cooling, adjusting pH with hydrochloric acid, stirirng uniformly, heating by water bath, adding the actived enzyme solution, mixing uniformly, performing enzymolysis, filtering, abandoning the filter to obtain medicinal material powder after enzymolysis, adding ethanol and fluxing for extraction, filtering, combining the filtrate, condensing under reduced pressure, recycling ethanol, and drying to obtain the Hypericum perforatum L extractive. The invention improves the content of hypericin in the extractive and the abandoned filtrate after enzymolysis takes away a large amount of water-soluble impurities so that the moisture of the extractive is not needed to absorb again. The biological method is safe, pollution free and has simple operation and is easy for industrialized application.