Background: Baihe Zhimu Tang (BZT) is a widely used traditional Chinese medicinal formula in treating various diseases; however, its active components have remained unknown. Materials and Methods: Based on the metabolic fingerprinting technique and liquid chromatography/diode array detection-electrospray ionization-mass spectrometry (LC/DAD-ESI-MS), a method for rapid screening and analysis of the multiple absorbed bioactive components and metabolites of an oral solution of Baihe Zhimu Tang (BZT) in rabbit plasma, urine and feces after oral administration of BZT was developed. Results: The results obtained from a comprehensive comparative analysis of the fingerprints of the BZT and its metabolic fingerprints in rabbit biological samples indicated that 19 components in the BZT were absorbed into the rabbit's body. Both of them were tentatively identified from their MS and UV spectra and retention behaviors by comparing the results with the reported literature. In addition, only six components were found in the metabolic fingerprints, which suggested that they might be metabolites of some components in the BZT. Conclusion: The findings demonstrated that the proposed method could be used to rapidly and simultaneously analyze and screen the multiple absorbed bioactive constituents and metabolites in a formula of traditional Chinese medicines (TCMs) by comparing and contrasting the chromatographic fingerprints with its metabolic fingerprints. This is very important not only for the pharmaceutical discovery process and the quality control of crude drugs, but also for explaining the curative mechanism of TCMs.