Targeting therapy of anti-cancer drugs has been gaining increasing attention. Cell pharmacokinetics have been used for in vitro disposition evaluation, as well as drug–drug interaction for anti-cancer drugs, revealing their fate after entering tumor. Flavonoid compound oroxylin A (OA) possesses strong anti-cancer effects especially on the liver and breast cancer. However, despite the low bioavailability, the disposition of OA and its active metabolite in the target cancer cells remained unclear. In current study, a highly sensitive and selective solid phase extraction (SPE)-UPLC–MS/MS method was developed and validated to simultaneously quantify the concentrations of OA and its major active metabolite oroxylin A 7-O-d-glucuronide (OG) in HepG2 cell lysate and multiple subcellular organelle fractions. The proposed method appeared to be suitable for the analysis with desirable linearity(R2>0.99). The relative standard deviations (RSDs) of intra- and inter-assay precision and accuracy were less than 9.9% and −7.7%, 8.4% and 11% for OA and OG in cell lysate respectively. The intra- precision and accuracy was less than 9.5% and −11.3%, 9.4% and 12.3% for OA and OG in subcellular organelles respectively. The range of absolute recovery of this method in the cell lysate was from 73.1%±1.4% to 87.9%±6.7%. The RSDs of matrix effects of the quality control (QC) samples were below 15%. The uptake and distribution experiments demonstrated a time-dependent transport characteristic in HepG2 cell lines. Furthermore, both OA and OG were mainly distributed into nuclei after taken up by the tumor cells. In addition, OG was also distributed into mitochondria, which indicates another potential target of OG. The present study, for the first time, reports the in vitro cell pharmacokinetics profiles of OA and OG in tumor cell lines in vitro.