As the main active component of Panacis majoris Rhizoma, Chikusetsu saponin IVa has the activity of anti-oxidation, anti-inflammatory pain, and so on.Obtaining high purity Chikusetsu saponin IVa by simple purification steps is a prerequisite for its deep development. In this paper, the separation and purification of Chikusetsu saponin IVa were studied by molecular imprinting technique. By ultraviolet and visible spectrophotometry and computer molecular simulation, it was concluded that water-soluble 3-(2-carboxyethyl)-1-vinylimidazolium bromide ionic liquid was the best functional monomer compared with acrylic acid and acrylamide. The molecularly imprinted polymers were prepared by precipitation polymerization at 60°C with Chikusetsu saponin IVa as template molecule, 3-(2-carboxyethyl)-1-vinylimidazolium bromide as functional monomer, ethylene glycol dimethacrylate as cross-linker, 2, 2'-azobisisobutyronitrile as initiator, and ethanol as porogen. The properties of molecularly imprinted polymers were studied by scanning electron microscopy, Fourier transform infrared spectroscopy, thermo-gravimetric analysis, nitrogen adsorption/desorption isotherm, and X-ray photoelectron spectroscopy. The maximum adsorption capacity was 171.33 mg/g, and the imprinting factor was 2.6. Finally, the polymers can be successfully used in the purification of Chikusetsu saponin IVa from Panacis majoris Rhizoma through a simple procedure, the content was significantly increased. The recoveries of the spiked samples for the CS-IVa ranged from 94.05 to 99.95% with relative standard deviation values lower than 2.67%. The results showed that the polymers demonstrated good adsorption capacity for Chikusetsu saponin IVa. Meanwhile, the polymers showed great stability and reusability during the application.