The effects of pulse ultrasound with different pulse parameters on the breakthrough curves of Geniposide on Resin 1300 were studied. The mass transfer model describing the adsorption process was constructed. Adsorption capability and the overall mass-transfer coefficient were obtained by fitting the constructed mass-transfer model and the experimental data. The effects of pulse ultrasound on adsorption of Geniposide on Resin 1300 in a fixed bed were studied and compared. Amount of Geniposide adsorbed on Resin 1300 in the presence of ultrasound is lower than that in the absence of ultrasound, but the mass-transfer rate with ultrasonic irradiation is higher than that without ultrasound. Furthermore, mass transfer rate is enhanced by pulse modulation. In the conditions studied, the adsorption equilibrium constant decreases with increasing ultrasonic power, while the overall mass-transfer coefficient increases. With increasing pulse duty ratio, adsorption equilibrium constant decreases initially, reaches a minimum when pulse duty ratio is 0.5, and then increases. On the contrary, the overall mass-transfer coefficient increases initially and reaches a maximum when pulse ratio is 0.5, and then decreases. Effects of pulse period on adsorption equilibrium and mass transfer rate reached the peak at pulse period of 28.6 ms.