Calycopterin is a flavonoid compound isolated from Dracocephalum kotschyi that has multiple medical uses, as an antispasmodic, analgesic, anti-hyperlipidemic, and immunomodulatory agents. However, its biological activity and the mechanism of action are poorly investigated. Herein, we investigated the apoptotic effect of calycopterin against the human hepatoblastoma cancer cell (HepG2) line. We discovered that calycopterin-treated HepG2 cells were killed off by apoptosis in a dose-dependent manner within 24 h, and was characterized by the appearance of nuclear shrinkage, cleavage of poly (ADP-ribose) polymerase and DNA fragmentation. Calycopterin treatment also affected HepG2 cell viability: (a) by inhibiting cell cycle progression at the G2/M transition leading to growth arrest and apoptosis; (b) by decreasing the expression of mitotic kinase cdc2, mitotic phosphatase cdc25c, mitotic cyclin B1, and apoptotic factors pro-caspases-3 and -9; and (c) increasing the levels of mitochondrial apoptotic-related proteins, intracellular levels of reactive oxygen species, and nitric oxide. We further examined the phosphorylation of extracellular signal-related kinase (ERK 1/2), c-Jun N-terminal kinase, and p-38 mitogen-activated protein kinases (MAPKs) and found they all were significantly increased in HepG2 cells treated with calycopterin. Interestingly, we discovered that treated cells had significantly lower Akt phosphorylation. This mode of action for calycopterin in our study provides strong support that inhibition of PI3K/Akt and activation of MAPKs are pivotal in G2/M cell cycle arrest and apoptosis of human hepatocarcinoma cells mediated by calycopterin.