Abstract: Aim To establish a method to measure the inclusion constant of supramolecular compound by capillary electrophoresis. In addition, by employing this method to investigate the intensity of interaction of antibacterial sodium houttuyfonate and β-cyclodextrin, and to measure the stability constant of the inclusion compound formed. Methods The mobilities of houttuyfonate were measured in solutions with different concentrations of β-cyclodextrin by capillary electrophoresis. The stability constant of the inclusion compound was calculated by peak-shift model mathematically. Results The mobility of houttuyfonate shifts from its original value with the increased concentration of β-cyclodextrin. When the limit was reached, the mobility of sodium houttuyfonate did not change even by increasing the concentration of β-cyclodextrin. The reproducibility is well, and the logarithm of inclusion constant obtained was 3.81 regardless of β- cyclodextrin concentration added. The interaction of the sodium houttuyfonate and β-cyclodextrin is strong. If they blended at a radio of 1∶1, the transform rate of sodium houttuyfonate is 98%. The value of stability constant of supramolecular inclusion compound is independent of concentration of β-cyclodextrin. Conclusion This technique of capillary electrophoresis can be used to the measurement of inclusion constant of drug with β-cyclodextrin. Furthermore, it can be applied to research the stability of inclusion compound drugs in physiological condition.