The invention discloses a method for preparing flavonoid compounds from hypericum japonicum by means of extracting and separating. The method includes steps of adding hypericum japonicum medicinal materials into water with the quantity of 8-12 times the quantity of the hypericum japonicum medicinal materials in each procedure, extracting the hypericum japonicum medicinal materials for 0.5-1.5 hours under heating conditions in each procedure, extracting the hypericum japonicum medicinal materials by 2-4 times, filtering extracted liquid to obtain filter liquid, collecting and combining the filter liquid, and concentrating the filter liquid to obtain thick paste, namely, an extract A, of the hypericum japonicum medicinal materials; adding a certain quantity of ethyl alcohol or methanol into the extract A until the concentration of the ethyl alcohol or methanol is 60%-90%, uniformly mixing the ethyl alcohol or methanol with the extract A to obtain mixed liquid, allowing the mixed liquid to stand still and layer, then filtering upper liquor layers, recycling solvents and concentrating the upper liquor layers to obtain a semi-solid extract which is an extract B; adding the extract B into water with the quantity of 0.5-2.0 times the quantity of the extract B, uniformly stirring the extract B, filtering insoluble materials to obtain filter liquid, allowing the filter liquid to stand at the temperature of 0-30 DEG C for 2 hours at least, dissolving out precipitates, filtering the filter liquid, collecting filter cake and drying the filter cake to obtain the flavonoid compounds. The relative density of the thick paste of the hypericum japonicum medicinal materials is 1.10-1.40. The method has the advantages that the high-content flavonoid compounds can be extracted from the hypericum japonicum by the aid of 4 steps, the method is simple, convenient, practical and environmental friendly, and industrial production can be facilitated.