The contents of various elements in the fourth generation atractylodes macrocephala koidz cultivated by spaceflight breeding were analyzed and compared with those of the ground group on the whole jointly by XRF and PXRD. The results showed that the element Na and Ti could not be detected in the space group, and the levels of K and Mn were enhanced by 1.16 and 1.15 times as these elements were measured in ground group, but other elements’ contents declined to different degrees, and the most notable elements are Si and P, decreasing by 82.1% and 71.2% accordingly; there is some whewellite in the ground group, whereas much less is found in the space group, The ground group contains inulin, however none in the space group. Spaceflight breeding can harvest significantly mutated specific Chinese herbal medicines varieties. The combination of two testing techniques has a positive role in space breeding applied in cultivation of medicinal plants.