The stable isotopic composition of natural gas can be used to identify its origin and source. However, low concentrations of gaseous hydrocarbons in high-mature natural and shale gases hinder accurate determination of their compound- and position-specific isotopic compositions. In this study, an online C2+ hydrocarbon gas concentration system combined with gas chromatography–isotope ratio mass spectrometry (GC–IRMS) or gas chromatography–pyrolysis–gas chromatography–isotope ratio mass spectrometry (GC–Py–GC–IRMS) was developed to determine compound- and position-specific isotopic compositions of low-abundance gaseous hydrocarbons. The lower limit of the gas concentration required for isotope ratio determination using the online concentration system is 0.001% (0.003%) for compound-specific carbon (hydrogen) isotopes and 0.005% for position-specific carbon isotopes and is thus applicable to most natural gas samples. The online concentration technique does not cause significant isotopic fractionation effects, and the combination with GC–IRMS and GC–Py–GC–IRMS can accurately and precisely determine the compound-specific δ13C and δD values of low-content C2+ gaseous hydrocarbons and the position-specific δ13C values (δ13Ca, δ13Cb, and SP values) of propane in low-content propane samples, respectively. The application of our method to two natural gas samples from the Ordos and Sichuan basins further confirms that the online concentration method allows simple and rapid determination of the compound- and position-specific isotopic compositions of low-abundance gaseous hydrocarbons.