Clumped-isotope analysis provides new constraints on the formation and evolution of methane. High-resolution isotope-ratio mass spectrometry (HR-IRMS) is a sensitive, precise, and stable analytical technique increasingly used in methane clumped-isotope analysis. However, the lack of standard reference frames hinders the comparison of data from different laboratories and the evaluation of accuracy. In this study, an absolute reference frame was introduced for HR-IRMS analysis of the multiply substituted methane isotopologues 13CH3D and 12CH2D2. We evaluated the optimized performance of a Panorama (Nu Instruments, UK) HR-IRMS system by repeated analysis of an intra-laboratory standard gas, finding that these rare isotopologues can be analyzed separately with high precision, repeatability, and reproducibility. Internal precision (a key parameter in instrument performance) reached 0.15‰ − 0.25‰ for Δ13CH3D and 0.70‰ − 0.85‰ for Δ12CH2D2 values, ensuring the reliability of data. Comparison of results before and after purification demonstrated that purification procedures caused negligible isotopic fractionation of clumped isotopes. Isotopic-exchange experiments revealed source effects in the MS ion source, depending on the difference in bulk H isotopic composition between sample and reference gas, but independent of bulk C isotopic composition. To improve analytical accuracy for methane isotopologues, an absolute reference frame was developed through experiments involving a suite of mixed gases of different H isotopic composition equilibrated at 100 °C and a standard gas equilibrated at 2 °C–500 °C. Based on the reference frame, raw data were processed with a non-linearity correction and converted to real values with empirical transformation functions. The reference frame was applied to analyses of two methane standard gases and three natural gases from Tarim Basin, China. Measured Δ13CH3D and Δ12CH2D2 values for two standard gases were consistent with published values. Clumped-isotope signatures of natural gases preserve information related to the formation temperature of methane.