Cyperus rotundus is the dry rhizome of the Cyperaceae plant Cyperus. Although there are two types of processed products in clinics, their quality differences are not clear, and the identification methods are more complex. In this study, the chemical composition of different processed products of Cyperus rotundus was characterized using ultra-high-performance liquid chromatographyquadrupole-time of flight-mass spectrometry and molecular network analysis, to identify the potential chemical markers and to establish a quick and simple color-based discrimination method. Among the 65 compounds analyzed, 12 showed significant differences. Observing the color, the surface brightness (L*) of Cyperus rotundus decreased after vinegar processing, while red (a*) and yellow (b*) values increased. These color values correlated significantly with chemical compositions. Finally, a color discriminant function was established and verified for raw Cyperus rotundus and vinegar-processing Cyperus rotundus. Based on this study, Cyperus rotundus' quality can be effectively controlled and provides a method for the comprehensive characterization of chemical components and chemical markers of other traditional Chinese medicine and processed products, as well as new ideas and methods in identification and quality evaluation.