Modern agriculture contributes significantly to greenhouse gas emissions in several ways. From the perspective of sustainability assessment, it is not enough to evaluate mitigation measures that rely only on emissions reductions. In this article, we use the method of decoupling analysis to construct a decoupling index based on carbon footprint and crop yield and evaluate the relationship between crop production and greenhouse gas emissions using the most modern grain production base in China as a case study. The results indicate that a weak but variable decoupling trend occurred from 2001 to 2015 and that each branch achieved on average a weak decoupling across the study period. In addition, rice production constituted 80% of the regional carbon footprint in a crop's life cycle. The results of our analysis of rice production show that weak decoupling was the most common outcome but was not consistent because a weak coupling occurred in 2015. Each branch on average achieved a weak decoupling except for the SH branch. Our research indicates that high agricultural material inputs with low utilization efficiency contributed to the poor relationship between crop production and greenhouse gas emissions in the study area. Fertilizer, especially N fertilizer, was an important contributor to the total greenhouse gas emissions of crop production. As a supplement to carbon footprint assessment, this decoupling analysis helps local decision-makers diagnose the level of green growth, identify key options to mitigate greenhouse gas emissions from agriculture, and adopt more targeted interventions towards sustainable agriculture.