The invention provides a hepatitis B virus resistant active composition of polyprenols from ginkgo biloba leaves and a preparation method thereof. The method is characterized by taking the liposoluble ginkgo biloba leaves with polyprenol content being lower than 40% as the raw materials, adopting activated carbon and attapulgite clay with mass ratio of 1:(1-20) as a mixed decoloring agent, carrying out decoloring for 10-80min at 50-120 while stirring, carrying out medium-pressure column chromatographic separation on the decolored polyprenols until the purity of the polyprenols is over 90% andtaking ginkgo biloba flavonoids and terpene lactones as the auxiliary materials to prepare the active composition. The active composition has the effect of resisting hepatitis B virus and can be usedfor developing hepatitis B virus resistant drugs.