Rice is a staple food for many Asian countries; however, identifying climate-smart rice management practices has become increasingly important to fighting climate change. This study comprehensively evaluated the agronomic, environmental, and economic performance of various rice production techniques over two winter seasons (2020 and 2021), with a focus on sustainability and climate-smart agriculture. The evaluated methods included System of Rice Intensification with Alternate Wetting and Drying (SRI-AWD), Direct Seeded Rice with AWD (DSR-AWD), and Traditional Farmers’ Practices under Continuous Flooding (FPR-CF). Among these, SRI-AWD significantly outperformed the others, achieving up to 39.4% higher grain yield, enhanced straw yield, harvest index, and water productivity, while reducing total water use by 37.5%. DSR-AWD recorded the lowest energy inputs, and both SRI-AWD and DSR-AWD demonstrated the highest energy use efficiency. Greenhouse gas emissions—particularly methane—were substantially reduced under AWD-based systems, with SRI-AWD exhibiting the lowest global warming potential. Soil health indicators, including labile carbon fractions, microbial populations, and enzyme activities, were markedly improved under SRI-AWD, correlating positively with increased soil organic carbon and microbial activity. Regression analysis identified soil water-soluble carbon and bacterial populations as key determinants of yield, while methanogens and denitrifiers were the main drivers of greenhouse gas emissions. Economically, SRI-AWD yielded the highest gross and net returns (34.9% and 122% higher, respectively), along with the most favorable benefit–cost ratio and climate-smart index (CSI), reflecting higher productivity, climate resilience, and a more efficient use of resources. In contrast, FPR-CF proved to be the least sustainable option. Overall, SRI-AWD emerged as the most sustainable, profitable, and climate-smart rice cultivation strategy, offering a viable pathway toward resilient and eco-efficient rice production systems.