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Abstract Agricultural soils play a dual role in regulating the Earth's climate by releasing or sequestering carbon dioxide (CO₂) in soil organic carbon (SOC) and emitting non‐CO₂greenhouse gases (GHGs) such as nitrous oxide (N₂O) and methane (CH₄). To understand how agricultural soils can play a role in climate solutions requires a comprehensive assessment of net soil GHG balance (i.e., sum of SOC‐sequestered CO₂and non‐CO₂GHG emissions) and the underlying controls. Herein, we used a model‐data integration approach to understand and quantify how natural and anthropogenic factors have affected the magnitude and spatiotemporal variations of the net soil GHG balance in U.S. croplands during 1960–2018. Specifically, we used the dynamic land ecosystem model for regional simulations and used field observations of SOC sequestration rates and N₂O and CH₄emissions to calibrate, validate, and corroborate model simulations. Results show that U.S. agricultural soils sequestered Tg CO₂‐C year⁻¹in SOC (at a depth of 3.5 m) during 1960–2018 and emitted Tg N₂O‐N year⁻¹and Tg CH₄‐C year⁻¹, respectively. Based on the GWP100 metric (global warming potential on a 100‐year time horizon), the estimated national net GHG emission rate from agricultural soils was Tg CO₂‐eq year⁻¹, with the largest contribution from N₂O emissions. The sequestered SOC offset ~28% of the climate‐warming effects resulting from non‐CO₂GHG emissions, and this offsetting effect increased over time. Increased nitrogen fertilizer use was the dominant factor contributing to the increase in net GHG emissions during 1960–2018, explaining ~47% of total changes. In contrast, reduced cropland area, the adoption of agricultural conservation practices (e.g., reduced tillage), and rising atmospheric CO₂levels attenuated net GHG emissions from U.S. croplands. Improving management practices to mitigate N₂O emissions represents the biggest opportunity for achieving net‐zero emissions in U.S. croplands. Our study highlights the importance of concurrently quantifying SOC‐sequestered CO₂and non‐CO₂GHG emissions for developing effective agricultural climate change mitigation measures.