To investigate the mechanism in Scutellarein-induced apoptosis of SAS human tongue cancer cells, inhibitory effects of Scutellarein on SAS cells were detected by MTT assay. Cell apoptosis was analyzed by flow cytometry. Ultrastructural changes of SAS cells were observed by transmission electron microscopy (TEM). Mitochondrial transmembrane potential (ΔΨm) were analyzed by JC-1 [5,5,6,6-Tetrachloro-1,1,3,3-tetraethylbenzimidazolylcarbocyanine iodide]. Western blotting was used to examine the expression level of Bcl-2, Bax and caspase-3 in SAS cells treated with Scutellarein. Scutellarein inhibited the proliferation of SAS cells in a time and dose-dependent manner and increased the percent of apoptotic cells. The mitochondrial cristae were swollen and had vacuolar degeneration. ΔΨm decreased when the concentration of scutellarein increased. Scutellarein effectively up-regulated the expression of mitochondrial Bax and caspase-3 and down-regulated the expression of Bcl-2. Scutellarein induces apoptosis of SAS human tongue cancer cells via activating mitochondrial signaling pathway.