In this study the potential use of an aqueous two phase system (ATPS) for the extraction of two lignans from Phyllanthus Niruri L. was evaluated and optimized using response surface methodology (RSM). Their anti-cancer potential against human lung cancer cell line A549, hepatic cancer cell line SMMC-7721, gastric cancer cell line MGC-803 were also evaluated respectively. The result showed that lignan hypophyllanthin displayed obvious anti-cancer activity in all of three cell line, but lignan phyllanthin only performed significant activity against SMMC-7721 cell line. Besides, the MOE program docking research of two compounds inside the related protein active site was carried out to explore the molecular interactions and targets. The docking result explained protein 4ZSE (human lung cancer target protein), 4OUM (gastric cancer target protein), 3QBY (hepatic cancer target protein), 1RI0 (hepatic cancer target protein) might be potential active site. In briefly, this study exhibited the in vitro anti-cancer potential of two lignans and this new extraction method may also be applicable for other natural products.