Methane is a powerful greenhouse gas contributing significantly to global warming. South Asia is a major methane emission region, yet source-diagnostic isotopic signatures remain poorly constrained, limiting top-down source attribution. To address this gap, we conducted extensive sampling and isotopic analyses of major methane sources in South Asia. Our results reveal substantial deviations of South Asian methane source fingerprints from global means. Methane from C3 biomass burning is more depleted in δ¹³C (–30.9±2.2 ‰) but more enriched in δ²H (–201±18 ‰), while ruminant methane (C3) is strongly depleted in both δ¹³C (–68.7±0.5 ‰) and δ²H (–343±6 ‰). In contrast, rice paddy methane is more enriched in δ¹³C (–53.8±0.8 ‰) and δ²H (–311±6 ‰), with their ratios signaling pre-emission oxidation. Wastewater methane shows enriched δ¹³C (–45.0±2.4 ‰) and depleted δ²H (–350±10 ‰) relative to global means, with minimal oxidation or spatial variation. These pronounced regional differences highlight the importance of using regionally constrained source fingerprints in isotope-based source apportionment. A global synthesis further shows that δ¹³C signatures of biomass burning and ruminant methane are primarily controlled by C3/C4 feedstocks, whereas δ²H is relatively insensitive to substrate type. Methane from rice paddies and wetlands exhibits strong latitudinal gradients worldwide. Combining emission inventories with source-specific isotope fingerprints reveals a mismatch with atmospheric methane in South Asia, suggesting an overestimation of rice paddy emissions and/or an underestimation of other microbial sources. These findings demonstrate the utility of top-down dual-isotope constraints to refine regional methane budgets and mitigation strategies.