The invention discloses a method for microwave extracting houttuynia cordata chromocor, comprising following steps: drying houttuynia cordata and disintegrating to 60 order, adding 40% ethanol according to ratio between solid and liquid of 1: 40, immersing for 30 minutes, keeping microwave power be at 900W, irradiating for 40 seconds, cooling with ice water, irradiating for 40 seconds again, repeating the step for three times; decompression condensing ethanol extract, putting it into AB-8 macro-porous absorption resin, washing with water and then with 70% of ethanol, decompressing drying washing liquid and getting final product. The invention is characterized by simple process and convenient operation, no pollution, non toxicity, high extraction efficiency and higher product purity.