Agricultural activities constitute a major contributor to global greenhouse gas emissions,and their carbon emissions have garnered significant attention in addressing climate change and achieving sustainable development goals.. Within China's 'Dual Carbon' policy framework, investigating the carbon emission dynamics of agricultural production transformation is crucial for achieving the coordinated development of ecological environmental protection and low-carbon agricultural transformation. Focusing on Fujian Province—a national ecological civilization pilot zone in southern China's mountainous terrain,this study established a county-scale analytical framework, an evaluation index system for agricultural production transformation was constructed based on the "factor-structure-function" framework. By integrating a methodological framework combining emission factor analysis, composite indexing, and fixed-effects regression, this study analyzed the spatiotemporal patterns and characteristics of the change rate and emission intensity of agricultural carbon emissions in Fujian Province from 2006 to 2021. This study identified the types of agricultural production transformation, examined the transformation characteristics of each category, and explored the differences in carbon emissions and their influencing effects across different transformation categories. Key findings include: (1) Temporal trends showed the rate of change in agricultural carbon emissions in Fujian initially increased before declining, with emission intensity decreasing steadily (average reduction: 63.9%).(2)The agricultural production transformation in Fujian Province can be categorized into four categories, each with distinct characteristics that led to differentiated trends in carbon emissions.(3)The benchmark regression results indicated that the increase in cultivated land per laborer was a significant factor driving the rise in agricultural carbon emission intensity. The promotion of green and low-carbon technologies resulting from the increase in rural non-agricultural employment rates was the main driver for reducing agricultural carbon emission intensity. (4)Heterogeneity analysis revealed that technological innovation, appropriately scaled farming practices, and specialized modern agricultural systems emerged as viable decarbonization pathways for achieving the carbon emission reduction in regional agriculture. Finally, based on the research findings, the study proposed the following recommendations for achieving agricultural production transformation and carbon emission reduction in the hilly and mountainous regions of southern China: promoting region-specific agricultural production transformation tailored to local conditions, reducing the use of agricultural inputs in the hilly regions of southern China, and implementing targeted strategies to advance carbon emission reduction in each transformation zone.These recommendations emphasize the need for context-specific policies that address the unique challenges and opportunities of different regions, ensuring that emission reduction efforts are both effective and equitable.The research can provide scientific references for the differentiated development of low-carbon agriculture in various regions undergoing agricultural production transformation in the hilly and mountainous areas of southern China.