The reconstruction of land spatial planning and the increasing severity of carbon emissions pose significant challenges to carbon peak and carbon neutrality strategies. To establish low-carbon and sustainable agricultural spatial planning while achieving dual carbon strategy goals, it is essential to accurately analyze the mechanisms of agricultural spatial transfer and their carbon emission effects, as well as the key factors influencing carbon emissions from agricultural spatial transfer. Therefore, this study, based on land use remote sensing data from 2000 to 2020, proposes a carbon emission accounting system for agricultural space transfer. The carbon emission total from agricultural space transfer in the Harbin-Changchun urban agglomeration over the 20-year period is calculated using the carbon emission coefficient method. Additionally, the spatiotemporal patterns and influencing factors are analyzed using the standard deviation ellipse method and the geographical detector model. The results indicate that: (1) The agricultural space in the Harbin-Changchun urban agglomeration has increased, with a reduction in living space and an expansion of production space. Among land type conversions, the conversion between cultivated land and forest land has been the most intense. (2) The conversion of agricultural space to grassland and built-up land has been the primary source of net carbon emissions. The carbon emission center has shown a migration path characterized by “eastward movement and southward progression,” with a high-north to low-south distribution pattern. Significant carbon emission differences were observed at different spatial scales. (3) Natural environmental factors dominate the carbon emissions from agricultural space transfer, while socioeconomic and policy factors act as driving forces. Elevation is the primary factor influencing carbon emissions from agricultural space transfer. Interactions between factors generally exhibit nonlinear enhancement, with the interaction between elevation, annual precipitation, and industrial structure showing a strong explanatory power. Notably, the interactions between elevation, average annual precipitation, and industrial structure demonstrate significant explanatory power. These findings highlight the necessity for government action to balance agricultural spatial use with ecological protection and economic development, thereby providing scientific references for optimizing future land spatial structures and formulating regional carbon balance policies.