This paper describes the development of a gas chromatography–quadrupole mass spectrometry system attached to a differential-pumping-type environmental cell of the reaction science high-voltage electron microscopy instrument at Nagoya University to distinguish unambiguously between different gas species with the same mass-to-charge ratio. Several model experiments were used to verify the efficacy of the newly proposed system, confirming its ability to analye the atomic-level structural changes during heterogeneous catalysts and the associated gas-reaction kinetics simultaneously, providing new insights into operando measurements in the field of environmental transmission electron microscopy.