Abstract: Interactions between Apt29, bovine thrombin (B-Thr) and five active molecules in Dragon's blood were investigated based on capillary zone electrophoresis (CZE). The CZE conditions were set as following:effective capillary length of 40 cm, injection volume of 3.45 kPa, injection time of 5 s, voltage of +15 kV, temperature of 15℃, detection wavelength of 214 nm and 330 nm. The results show that K_b between Loureirin A and B-Thr is 4.73×10⁴ L/mol, and Loureirin B, Loureirin C, Resveratrol 7,4-dihydroxyflavanone are no bound with B-Thr obviously. The K_b between Loureirin B, DHF and Apt29 are 1.98×10⁴, 1.83×10⁴ L/mol, respectively. Loureirin A, Loureirin C and Resveratrol are no bound with Apt29 obviously. The study indicates the interactions between B-Thr, Apt29 and active molecules in Dragon's blood. It can provide a basis for speculating the potential binding site of dragon's blood with thrombin, and delivering Dragon's blood to thrombin with aptamer as target delivery tool.