To predict the pharmacodynamic fractions of Buyang Huanwu decoction, the imprinting properties of the "imprinting template" of the entire formula and its three different structural fractions of Buyang Huanwu decoction were compared and analyzed. The content of 32 components in the entire formula of Buyang Huanwu decoction and different structural fractions was measured and their molecular connectivity index (MCI) and MCI similarity was calculated. The UPLC fingerprint spectra of the entire formula of Buyang Huanwu decoction and different structural fractions was established. And the total statistical moment parameters and their similarity of the fingerprint spectra was calculated, and the "imprinting template" similarity between Buyang Huanwu decoction and different structural fractions was compared by combining MCI similarity and total statistical moment similarity. The similarity order of MCI between the entire formula and its different structural fractions is: glycoside>aglycone>alkaloid. There are significant differences in the number of peaks, the total first-order moment and information entropy in the entire formula and its various fractions of Buyang Huanwu decoction. The similarity order of the total moment between the entire formula and its different structural fractions is: glycoside>aglycone>alkaloid. There are differences in the imprinting patterns of each "imprinting template" of Buyang Huanwu decoction, and the similarity between the the "imprinting template" of glycoside and the entire formula is relatively high, which may be the most representative pharmacodynamic fraction of the entire formula. The total statistical moment method and MCI method were utilized to characterize the "imprinting template" of different structural fractions in the study, providing a basis for the creation of multi-component Chinese medicine from Buyang Huanwu Decoction.