In this investigation, a novel chemometric method is developed for the analysis of five possible relationships of components or spectral features between two correlative but different hyphenated chromatographic systems. It is very helpful for comparison study of components present in different complex systems in both chemistry and systems biology. The proposed method, named alternative moving window factor analysis (AMWFA), could be utilized to determine the number of common components between different samples and then to identify their corresponding spectra half-automatically. AMWFA can alternatively be employed to mind for the selective information hiding in anyone of the two compared data X and Y, and to self-verify the resolution results by changing the extracted target matrices in analysis. From the results of comparison of simulated hyphenated chromatographic data, volatile chemical components in drug pair rhizoma ligustici chuanxiong-radix paeoniae rubra (RLC-RPR) and its single herbal medicines, and analysis of Angelica oral solution and its plasma sample after oral intake to rabbit, powerful ability of the proposed method is shown.