Tri-step identification of Fourier transform infrared spectroscopy (FTIR) integrated with second derivative spectroscopy and two dimensional correlation infrared spectroscopy (2D-IR) were applied to analyze and evaluate the alcoholic extracts and corresponding residues of cistanche deserticola from the surface to what lies behind. It was found that active compounds including phenylethanoid glycosides were enriched effectively after alcoholic extraction and the extract by using 70% of alcohol had the highest concentration compared to the others. The technique of the tri-step identification holistically disclosed the profile of active compounds in cistanche deserticola extracted by a series of concentrations of ethanol and validated the rationality of the traditional alcoholic extraction method. It not only could be used in monitoring the process of the alcoholic extraction and the compositions of the extracts and residues, discriminating micro-differences among them, but also could provide a macroscopic guidance for medicinal and pharmacological studies.