An isotope-ratio-monitoring gas chromatography-mass spectrometry apparatus and method are disclosed which provide for on-line analysis of isotope compositions with high precision. With the apparatus and method, samples are introduced in a hydrogen carrier gas into a gas chromatograph and resolved into discrete compounds. The discrete compounds are thereafter introduced to a selectively permeable membrane separator, empolying palladium, palladium alloy or other suitable material, to separate out the hydrogen carrier. A replacement carrier gas is simultaneously introduced to carry the chromatographic sample to a combustion reactor, water separator and isotope-ratio-monitoring mass spectrometer. The replacement carrier gas is introduced at a lower flowrate than the hydrogen carrier gas, thus permitting lower flowrates to be introduced to the mass spectrometer to improve its precision. Flowrates to the mass spectrometer are thus reduced without any loss or fractionation of the sample. An improved combustion system is employed to reduce system volume and equalize system pressure, while still providing quantitative combustion.