The U.S. rice paddy systems play an increasingly vital role in ensuring food security, which also contribute massive anthropogenic non-CO2 (CH4 and N2O) greenhouse gas (GHG) emissions with expanding cultivation area. Yet, the full assessment of GHG balance, considering trade-offs between soil organic carbon (SOC) sequestration and non-CO2 GHG emissions, is lacking. Integrating an improved agricultural ecosystem model with a meta-analysis of multiple field studies, we found that U.S. rice paddy was a rapidly growing net GHG emission source, increased 138% to 8.88 ± 2.65 Tg CO2eq yr-1 in the 2010s. CH4 emission made the most significant contribution (10.12 ± 2.28 Tg CO2eq yr-1) to this increase in net GHG emissions in the 2010s, but increasing N2O emissions, accounting for ~2.4% (0.21 ± 0.03 Tg CO2eq yr-1), cannot be ignored. SOC sequestration could offset about 14.0% (1.45 ± 0.46 Tg CO2eq yr1) of the climate-warming effects of soil non-CO2 GHG emissions in the 2010s. The aggravation of net GHG emissions stemmed from intensified land use/cover changes, rising atmospheric CO2, and heightened synthetic N fertilizer and manure application. Climate change exacerbated around ~21% of soil N2O emissions and ~10% of soil CO2 release in the 2010s. Nonetheless, adopting no/reduced tillage resulted in a substantial decrease of ~10 % in net soil GHG emissions, and non-continuous irrigation exhibited the potential to mitigate around 39% of soil non-CO2 GHG emissions. Great potential for emissions reduction in the mid-South U.S. by optimizing synthetic N fertilizer and manure ratios, reducing tillage, and implementing non-continuous irrigation.