Abstract: The components of Chinese medicine water extract are complex. With the development of traditional Chinese medicine pharmacy, it is urgent to establish a simple and effective separation and purification method for traditional Chinese medicine. Membrane separation technology, as a simple, direct and efficient material separation method, is widely used in the separation and purification of traditional Chinese medicine because of its low energy consumption and no secondary pollution. Using the ion-track etched membrane with different pore diameters to filter the Chinese medicine water extract in multiple steps, and characterizing the filtrate. The impurities above 1 μm can be removed through microfiltration without changing the properties of water extract. Besides, the proteins and starches can also be removed through ultrafiltration. After modification, the active components of traditional Chinese medicine, like paeoniflorin and chlorogenic acid, can be separated by the ion-track etched membrane. The results show that the ion-track etched membrane can be applied to the process of separation and purification of Chinese medicine water extract, which proves that the ion-track etched membrane can be used for the separation and purification of Chinese medicine water extract.