[Objective] To analyze the temporal and spatial characteristics of net carbon emissions from agriculture at the county scale in Fujian Province, with a view to providing a reference basis for the formulation of carbon emission reduction countermeasures in Fujian Province and other provinces and municipalities. [Methods] We constructed an accounting inventory of agricultural carbon emissions based on 12 carbon sources in plantation and livestock industries, and measured the total agricultural carbon emissions by using the carbon emission factor method; selected seven major crops to calculate the carbon uptake by combining with the agricultural characteristics of Fujian Province; and analyzed the spatial and temporal characteristics of the net agricultural carbon emissions in Fujian Province from 2001 to 2020 by using the exploratory spatial analysis method. [Results] ① During the study period, the net carbon emissions showed an inverted "V" trend of first increasing and then decreasing. In terms of carbon sources, carbon emissions from agricultural land use accounted for a larger proportion; in terms of carbon sinks, rice, vegetables and sugarcane contributed more to carbon sequestration. The intensity of agricultural carbon emissions in most counties (cities) showes a decreasing trend, but the average annual decline is small. ② There is a significant global spatial positive correlation of carbon emissions in counties in Fujian Province, showing spatial agglomeration characteristics, and the agglomeration pattern is dominated by high-high and low-low agglomeration. The spatial distribution pattern of the intensity of agricultural carbon emissions changes considerably, with an overall decreasing trend, in which about half of the counties (cities) are in the lower intensity zone. ③ The spatial class distribution pattern of counties (cities) in Fujian Province from 2001 to 2020 has changed to a certain extent, with an increase in the number of medium-emission zones and medium-low-emission zones, and a decrease in the number of high-emission zones, medium-high-emission zones and low-emission zones, and the polarization has been alleviated. [Conclusion] In recent years, most counties inFujian Province have shown a decreasing trend in agricultural carbon emissions and carbon emission intensity, and carbon emission reduction has achieved certain results, but the decline is not large, the future should also be from the policy incentives, optimization of industrial structure and other aspects of the measures taken to strengthen the effect of emission reduction, and to promote the transformation of agriculture low-carbon.