Abstract: Land fragmentation is a phenomenon of dispersed cultivated land distribution in household production under resource constraints. Due to the decentralization of operational scale, it increases redundant inputs, raises production costs, and hinders improvements in agricultural production efficiency. The heightened frequency of production and inputs often leads to increased agricultural carbon emissions, thereby impeding high-quality agricultural development. Against this backdrop, integrating the relationships among land fragmentation, agricultural production efficiency, and agricultural carbon emissions to clarify their mechanisms is crucial for reducing agricultural carbon emissions and enhancing production efficiency. In light of this, this study employs land-use data, agricultural input-output data, and agricultural carbon emission data from 2011 to 2020 in China’s three northeastern provinces to construct an evaluation system and a mediating effect model, investigating the relationships and mechanisms among the three variables. First, ArcGIS and Fragstats landscape pattern software were used to calculate land fragmentation, the DEA-SBM model was applied to measure agricultural production efficiency, and the Topsis entropy method was utilized to weight and compute agricultural carbon emissions. Second, a two-way fixed effects model and a mediating effects model were adopted to analyze the relationships among land fragmentation, agricultural carbon emission intensity, and agricultural production efficiency. Finally, heterogeneity analyses were conducted based on urbanization rates and rural residents’ income levels. The findings reveal: 1) Land fragmentation in northeastern China fluctuated between 2011 and 2020, with higher fragmentation in western regions and lower levels in northern areas. Agricultural production efficiency showed an upward trend in eastern and southern regions, with efficiency significantly higher in the east than in the west. Overall agricultural carbon emissions declined, with higher emissions in the west and lower levels in the north; 2) Land fragmentation has a significant positive impact on agricultural carbon emissions, with increased fragmentation elevating emissions. Agricultural production efficiency plays a mediating role in this process, accounting for 15.3% of the mediation effect; 3) The promoting effect of land fragmentation on agricultural carbon emissions is stronger in regions with higher urbanization rates and rural income levels. Therefore, it is recommended to enhance land resource consolidation, promote large-scale intensive agricultural management models, advance low-carbon and high-efficiency agricultural development, reduce agricultural carbon emissions, and achieve high-quality agricultural growth.