Revelation of chlorine and bromine isotope fractionation of halogenated organic compounds (HOCs) in electron ionization mass spectrometry (EI-MS) is crucial for compound-specific chlorine/bromine isotope analysis (CSIA-Cl/Br) using gas chromatography EI-MS (GC-EI-MS). This study systematically investigated chlorine/bromine isotope fractionation in EI-MS of HOCs including 12 organochlorines and 5 organobromines using GC-double focus magnetic-sector high resolution MS (GC-DFS-HRMS). Chlorine/bromine isotope fractionation behaviors of the HOCs in EI-MS showed varied isotope fractionation patterns and extents depending on compounds. Besides, isotope fractionation patterns and extents varied at different EI energies, demonstrating potential impacts of EI energy on the chlorine/bromine isotope fractionation. Hypotheses of inter-ion and intra-ion isotope fractionations were applied to interpreting the isotope fractionation behaviors. The inter-ion and intra-ion isotope fractionations counteractively contributed to the apparent isotope ratio for a certain dehalogenated product ion. The isotope fractionation mechanisms were tentatively elucidated on basis of the quasi-equilibrium theory. In the light of the findings of this study, isotope ratio evaluation scheme using complete molecular ions and the EI source with sufficient stable EI energies may be helpful to achieve optimal precision and accuracy of CSIA-Cl/Br data. The method and results of this study can help to predict isotope fractionation of HOCs during dehalogenation processes and further to reveal the dehalogenation pathways.