The transmembrane transport and distribution characteristics of emodin-β-CD inclusion complex in the nasopharyngeal carcinoma CNE-1 cells are observed using laser scanning confocal microscope. The results show that both emodin and emodin-β-CD inclusion complex are mainly distributed in the cytoplasm in granules. In the concentration range of 5~40 mg·L-1, the intake of emodin-β-CD inclusion complex nonlinearly increases with the increase of concentrations. Compared with the control group, emodin-β-CD inclusion complex uptake in cells is significantly lower than that of treatment with NaN3 and mannitol. After treatment with P-glycoprotein inhibitors cyclosporin A (CsA), intake of emodin-β-CD inclusion complex at low concentrations (smaller than 5 mg·L-1) significantly increases, but at high concentrations, intake of emodin-β-CD inclusion complex significantly decreases. Emodin-β-CD inclusion complex has long time of maintaining high concentration in cell relative to emodin. The mechanism of emodin-β-CD inclusion complex uptake in cells may involve energy-dependent endocytosis and P-glycoproteins participates in the conveying process of emodin-β-CD inclusion complex in CNE-1 cells. It provides a reference to improving emodin formulations.