Korean Citrus aurantium L. has long been used as a traditional medicine for the treatment of various cancers such as those of lung and prostat. C. aurantium L. has been reported to have anti-metastasis properties in in vitro experiments. However, the anti-metastasis effect of C. aurantium L. in vivo is not well understood. This study investigated the anti-metastatic effect of flavonoids isolated from Korean C. aurantium L. using high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS) in NOD/SCID mice. PKH-26 staining and immunohistochemical analyses indicated that flavonoids prevented cancer cell infiltration and localization to the lung. Also, flavonoids induced cancer cell apoptosis through the regulation of the apoptosis related protein cleaved caspase-3 and p-p53. In vitro results also show that flavonoids inhibited A549 cells metastasis and induced apoptosis. Moreover, proteomic analysis indicated comparable down-regulation of the Ddx3x and ANP43B proteins with control group after treatment with flavonoids. These results provide scientific support for the use of flavonoids isolated from C. aurantium L. for the treatment of human lung cancer.