Abstract: Balanophora involucrateHook. f. is a rare medicinal herb with a long history of clinical use in the western Hubei region. However, comprehensive and systematic comparative analyses of its chemical components in different medicinal parts are lacking. In this study, HPLC-MS/MS technology was applied to establish the chemical fingerprints of the rhizome, flower stem, and inflorescence of 10 batches ofB. involucratefrom five production areas in western Hubei. In total, 29 common peaks were calibrated, and the chemical structures of 27 chromatographic peaks were tentatively identified, including 13 phenolic acids and eight flavonoids. Cluster analysis (CA) and principal component analysis (PCA) revealed significant differences in chemical compositions between the underground (rhizome) and aboveground(flower stem, inflorescence) parts, while differences in chemical compositions between the flower stem and inflorescence were relatively small. The variable importance in projection (VIP) values in orthogonal partial least squares discriminant analysis (OPLS-DA) indicated that peaks 12, 8, 2, 3, 17, 21, 9, and 22 were potential quality markers (Q-markers) among different medicinal parts and could serve as the chemical basis for quality control.