In this study, the investigation of the volatile compounds of dried rhizomes of Coptis chinensis Franch, C. deltoidea C. Y. Cheng et Hsiao, and C. teeta Wall was carried out to complete the chemical composition of these valuable natural products. Volatile profiles were established and compared after headspace solid-phase microextraction (HS-SPME) using a polydimethylsiloxane/divinylbenzene (PDMS/DVB, 65 μm) fibre coupled to comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS). Analyses were performed and compared on two column-phase combinations (non-polar/polar and polar/non-polar). The majority of the identified compounds eluted as well-separated (pure) components as a result of high-resolution capability of the GC×GC method, which significantly reduces co-elution. Therefore, this increases the likelihood that pure mass spectra can be obtained. More than 290 volatile and semi-volatile organic compounds were tentatively characterized by means of GC×GC in tandem with TOFMS detection. Improved result interpretations were obtained in terms of compound classification based on the organized structure of the peaks of structurally related compounds in the GC×GC contour plot. These compounds are distributed over the chemical groups of hydrocarbons, acids, alkenes, alkynes, aldehydes, ketones, alcohols, esters, furans, and terpenoids. Among all the chemical groups, terpenoids present the higher number of identified compounds (44), alkenes (41), and aldehydes and ketones (28). This study completed the volatile phytochemical analysis of the headspace composition of various Coptis species rhizomes, and should serve as a means to identify the difference between the rhizomes and may also be useful to confirm individual species based on their volatile chemical profile.