The Tarim Basin is one of the most complex, ancient, and petroliferous deep craton basins in the world. Multiple sets of source rocks, stages of tectonism, and episodes of hydrocarbon generation and accumulation complicate the formation and evolutionary processes of hydrocarbons in the basin, especially for the deeply buried petroleum system at >6000 m depth. Paired clumped isotopes (Δ13CH3D and Δ12CH2D2) allow the investigation of methane isotopic bond ordering, elucidating the methane generation mechanism and its post-generation processes, which can complement studies of the molecular and conventional stable isotopic compositions of gas hydrocarbons in constraining the origin and source of natural gas. This study focused on methane clumped isotopes, and chemical and conventional stable isotopic compositions of natural gas samples from four typical oil and gas regions of the Tarim Basin. Results indicate that these gases are thermogenic gases with relatively high stable isotopic δ values (i.e., −46.1‰ < δ13C–CH4 < −25.9‰, −184‰ < δD-CH4 < −140‰). Most exhibit equilibrium methane clumped isotope signatures at temperatures of 128–257 °C, consistent with the main oil-window to gas-window region. The clumped isotope apparent temperature of equilibrated methane was used to determine its formation temperature, which was applied for gas–source correlations and thermal maturity assessments of the natural gases based on the results of previous basin modeling. The clumped isotope compositions of two gas samples from the Keshen area of the basin are characterized by significant deficits in Δ12CH2D2 values but with similar Δ13CH3D values to those of other equilibrated gases there, indicating the possibility of methane bond re-ordering at high temperatures (>300 °C) exceeding the methane “closure temperature”. Non-equilibrium gases in the Tabei area yielded a plausible Δ13CH3D apparent temperature (<160 °C) with a pronounced deficit in Δ12CH2D2 values, possibly owing to irreversible chemical kinetic processes in thermal cracking of organic matter at early thermal maturity (Ro < 1.5‰) or mixing between thermogenic gases generated at two distinct temperatures (i.e., ∼200 °C and ∼120 °C). Equilibrium clumped isotope signatures also rule out the possible effects of secondary alteration on natural gases in the Hetianhe area that were previously considered in conventional isotope studies. Such findings demonstrate that methane clumped isotopes provide independent and effective indicators of gas–source correlations in deep basins while also elucidating secondary processes that are often under- or over-estimated in conventional stable isotope studies.