Five fractions were split for the chemical components of Atractylodis macrocephalae rhizome by the combination application of various separation methods and the over 90% similarity of HPLC fringerprints within each fractions indicated the good repeatability for the splitting procedure. Further, a term of nonsimilarity degree ( NSD) was introduced to measure the unoverlapping property of the chemical fractions and different statistic analyses, including principal component analysis, cluster analysis, angle cosin analysis, squared euclidean distance and the NSD of peak areas of crude drug were used to qualitatively and quantitatively analyze their unoverlapping property, revealing the NSD among different fractions was calculated above 85%. Among them, the NSD of peak area of crude drug established on the basis of HPLC fingerprints of crude drug is more suitable for the NSD evaluation of chemical splitting fractions of crude drug comparing with other statistical methods and practical for reflecting the real content-activity relationship in the subsequent exploration of effective substances of crude drugs. This research provides a new effective method to evaluate the chemical difference of splitting fractions of Chinese medicine and lay the foundation for exploring the effective and property-flavor substances or of Atractylodes macrocephala Koidz.