The processing technology employed in traditional Chinese medicine (TCM) is significant and distinct. Meanwhile, the processed Coptis chinensis Franch. are significant in clinic based on clinical practice and literature. The current study used ultraperformance liquid chromatography method (UPLC) coupled with quadrupole time of flight mass spectrometry (qTOF/MS) and Marklynx software to analyze the chemical profiles of crude and processed C. chinensis Franch. 13 compounds in these samples are identified, including 3 compounds that are detected in C. chinensis Franch. for the first time. Moreover, the results of the experiment show significant chemical differences between crude and processed C. chinensis Franch. with principal component analysis (PCA). The obvious separation in PCA confirms the traditional processing theory in TCM.