Rice cultivation is a major source of methane (CH₄) emission in the agricultural sector, with a significantly higher global warming potential than carbon dioxide. Accurate and scalable quantification of CH₄ from rice paddies is essential for carbon accounting. This study presents an automated framework for estimating rice CH₄ emissions from irrigated paddies in the central plain of Thailand, integrating multi-sensor Synthetic Aperture Radar (SAR) observations with the IPCC methodology. The framework combines Sentinel-1 C-band SAR time series for phenological detection, ALOS-2 PALSAR-2 L-band full-polarimetric SAR for water regime classification, and IPCC water-scaling factors corresponding to Continuous Flooding, Single Drainage, or Multiple Drainage regimes. Evaluated across five stratified holdout sets, the phenology detection algorithm achieved planting and harvesting date Mean Absolute Errors of 6.1 ± 1.4 and 8.3 ± 1.7 days, with a 97.0% ± 2.7% operational detection rate. Water regime classification employed rice growth stage-specific Support Vector Machine classifiers with Radial Basis Function kernels (SVM-RBF), achieving per-stage test Balanced Accuracy ranging from 0.59 to 0.89. End-to-end integration using a four-track counterfactual decomposition yielded a full-pipeline mean absolute error of 18.5 ± 4.5 $\mathrm{kg}{\mathrm{CH}}_4{\mathrm{ha}}^{-1}$ (21.4% of the mean ground-based CH₄ calculation) and a mean bias of 3.5 ± 5.8 $\mathrm{kg}{\mathrm{CH}}_4{\mathrm{ha}}^{-1}$. Water level classification was confirmed as the dominant algorithmic uncertainty source, while the IPCC Tier 1 emission factor structural range (−32% to +48% of the default) exceeded all algorithmic errors combined. The proposed framework provides a spatially explicit approach for integrating multi-frequency SAR data into IPCC-compliant methane estimation, supporting Monitoring, Reporting, and Verification applications.