It has been reported that isotope fractionation can occur on gas chromatography (GC), yet little is known about concurrent dual-elements isotope fractionations on GC. Revelation of concurrent two-dimensional carbon and chlorine/bromine isotope fractionations of halogenated organic compounds (HOCs) on GC may be of important significance for compound-specific isotope analysis (CSIA). This study presents an in-depth investigation of the two-dimensional C and Cl/Br isotope fractionations of HOCs on GC using GC-double focus magnetic-sector high resolution mass spectrometry (GC-DFS-HRMS). The two-dimensional C and Cl/Br isotope fractionations of four organochlorines and four bromobenzenes on GC were simultaneously measured by GC-DFS-HRMS. The isotope fractionations were evaluated with isotope ratios, relative variations of isotope ratios (△hE) and isotope fractionation extents (ΛhE). All the HOCs exhibited significant inverse C and Cl/Br isotope fractionations, with Λ13C of 38.14‰–307.56‰, Λ37Cl of 59.60‰–146.85‰, and Λ81Br of 25.89‰–142.10‰. The isotope fractionations were significant in both ends of chromatographic peaks, while the isotope ratios in center retention-time segments were the closest to comprehensive isotope ratios in the whole peaks. Significant correlations between C isotope fractionation and Cl/Br isotope fractionation were observed, indicating that the isotope fractionations might have strong relationships and/or be dominated by similar factors. Relevant mechanisms for the two-dimensional C and Cl/Br isotope fractionations were tentatively proposed on basis of a modified two-film model and the theories related to zero point energy. The results of this study gains new insights into concurrent two-dimensional isotope fractionation behaviors of HOCs during physical processes, and are conducive to CSIA studies involving C, Cl and Br for obtaining high-quality data, particularly to dual-elements CSIA of C and Cl/Br.