In the conventional microscopic identification of traditional Chinese medicines (TCMs), disadvantages, such as rigid sample preparations and adding extra reagents which may result in structure information loss limit its application. X-ray phase contrast imaging (XPCI) was introduced to study the microscopic identification of Panax quinquefolium and Panax ginseng, in the aspects of clusters of calcium oxalate, vessels, cork cells, phloem and xylem rays. The experimental results show that XPCI method is convenient for microscopic identification. It is expected that XPCI will provide a new practical method for the identification of TCMs without any special sample treatments. The experiments also reveal that the phloem and xylem rays of Panax quinquefolium and Panax ginseng are obviously different. This microstructure difference may add another important basis for the microscopic identification of different ginsengs.