The invention relates to the technical field of medicines, and discloses a method for preparing high-purity rutin via a two-dimensional liquid chromatography-mass spectrometry combined technology. The method comprises the following steps of: adopting the two-dimensional liquid chromatography-mass spectrometry combined technology, taking methanol-water or acetonitrile-water as a mobile phase, using a reversed chromatographic column as the first dimension for preparing a chromatographic column, performing component cutting on a ginkgo leaf extract, and collecting a target component, namely, a rutin crude product; and using the reversed chromatographic column as the second dimension for preparing a chromatographic column, performing component cutting on the rutin crude product under the guide of a mass spectrometry selected ion peak, collecting, rotationally evaporating and concentrating, and then obtaining the high-purity rutin having a purity which can achieve more than 80%. In the method disclosed by the invention, heating is not needed, so that the doping of a hydrolysate is avoided; the preparation is simple in process, high in repeatability, and good in operability; simultaneously, ginkgo leaves are abundant in resource and easy to obtain, thus reducing the cost; and the method is suitable for large-scale production.