U.S. rice paddies, critical for food security, are increasingly contributing to non‐CO₂greenhousegas (GHG) emissions like methane (CH₄) and nitrous oxide (N₂O). Yet, the full assessment of GHG balance, considering trade‐offs between soil organic carbon (SOC) change and non‐CO₂GHG emissions, is lacking. Integrating an improved agroecosystem model with a meta‐analysis of multiple field studies, we found that U.S.rice paddies were the rapidly growing net GHG emission sources, increased 138% from 3.7±1.2TgCO₂eqyr⁻¹in the 1960s to 8.9±2.7TgCO₂eqyr⁻¹in the 2010s. CH₄, as the primary contributor, accounted for 10.1±2.3TgCO₂eqyr⁻¹in the 2010s, alongside a notable rise in N₂O emissions by 0.21±0.03TgCO₂eqyr⁻¹. SOC change could offset 14.0% (1.45±0.46TgCO₂eqyr⁻¹) of the climate‐warming effects of soil non‐CO₂GHG emissions in the 2010s. This escalation in net GHG emissions is linked to intensified land use, increased atmospheric CO₂, higher synthetic nitrogen fertilizer and manure application, and climate change. However, no/reduced tillage and non‐continuous irrigation could reduce net soil GHG emissions by approximately 10% and non‐CO₂GHG emissions by about 39%, respectively. Despite the rise in net GHG emissions, the cost of achieving higher rice yields has decreased over time, with an average of 0.84±0.18kgCO₂eqha⁻¹emitted per kilogram of rice produced in the 2010s. The study suggests the potential for significant GHG emission reductions to achieve climate‐friendly rice production in the U.S. through optimizing the ratio of synthetic N to manure fertilizer, reducing tillage, and implementing intermittent irrigation.