Abstract: Land fragmentation is the phenomenon of dispersed cultivated land distribution in household production under resource constraints. Decentralization of the operational scale increases redundant inputs, raises production costs, and hinders improvements in agricultural production efficiency. Increased frequency of production and input often leads to increased agricultural carbon emissions, thereby impeding high-quality agricultural development. Against this backdrop, integrating the relationships between 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 employed land use, agricultural input-output data, and agricultural carbon emission data from 2011 to 2020 in the three provinces of Northeast China to construct an evaluation system and a mediating effect model to investigate 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 used 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 income levels of rural residents. The findings revealed: 1) Land fragmentation in northeastern China fluctuated between 2011 and 2020, with higher fragmentation in the western regions and lower levels in the northern areas. Agricultural production efficiency showed an upward trend in the eastern and southern regions, with efficiency being 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 had a significant positive impact on agricultural carbon emissions, with increased fragmentation-elevating emissions. Agricultural production efficiency played 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 was 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 carbon emissions, and achieve high-quality agricultural growth.