Abstract: The purpose of this paper was to investigate the best conditions of extracting the total flavonoids content for Frutus Xanthii and Hypericum japonicum, and make a comparison about the total flavonoids in two plants. Using the way of ethanol reflux condensation and applying rutin as the standard, L9(34) was adopted to confirm the best optimum extraction process condition extracting of active ingredients. The experimental results showed that the Xanthium optimum extraction conditions was the ethanol concentration of 60% , extraction temperature of 70℃, extraction time of 4 h, and solid-liquid ratio of 1:30. Hypericum japonicum optimum extraction conditions for the ethanol concentration of 50%, extraction temperature of 80℃, extraction time of 1 h, solid-liquid ratio of 1:50 was obtained. In accordance with the best conditions of operation, optimum extraction process of total flavonoids extraction rate of Frutus Xanthii was 3.89% and rate of Hypericum japonicum was 4.31% by extraction rate as the indexes. The experimental results showed that the flavonoids of Hypericum japonicum were higher than Frutus Xanthii. This extraction technology was simple and feasible, and had better reference value.