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• Deans-switch is used to avoid complex preparation and losses of trace samples. • Baseline separation of crocetane and phytane is achieved (R >1.5) by 2D-GC technique. • First accurate determination of δ13C of crocetane in natural samples by 2D-GC-IRMS. Compound-specific isotope analysis of crocetane in sediments can be used to determine its origin. However, the co-elution of crocetane with phytane and complex substrates hinders the accurate determination of its isotopic composition. A heart-cutting two-dimensional gas chromatography–isotope ratio mass spectrometry (2D-GC–IRMS) method was developed to determine δ13C values of crocetane. Full chromatographic separation of crocetane was achieved with a 30 m CycloSil-B chiral capillary first column and a 60 m Chiraldex B-pH capillary second column (two series-connected 30 m Chiraldex B-pH capillary columns). Analyses of standard mixtures confirmed that the new method has satisfactory accuracy (deviations from the authentic values <0.5‰) and precision (RSDs <5%) for carbon isotope analyses of crocetane and phytane. The application of the method to two sediment samples indicates that baseline resolution is achieved (R >1.5) for crocetane and phytane, with 13C-depleted crocetane (δ13C values of −119.5‰ and −111.5‰ in the two natural samples, respectively) being an indicator of anaerobic oxidation of methane in cold seep areas. The new 2D-GC–IRMS method allows simple and efficient determination of the compound-specific carbon isotopic compositions of crocetane. [ABSTRACT FROM AUTHOR]