[Objective] The temporal and spatial characteristics of net carbon emissions from agriculture at county scale in Fujian Province were analyzed in order to provide references for the formulation of carbon emission reduction countermeasures in Fujian Province and in 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. We selected seven major crops to calculate carbon uptake by combining with the agricultural characteristics of Fujian Province. We 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 at most counties (cities) showed a decreasing trend, but the average annual decline was small. ② There was a significant global spatial positive correlation of carbon emissions at counties in Fujian Province, showing spatial agglomeration characteristics. The agglomeration pattern was dominated by high-high and low-low agglomeration. The spatial distribution pattern of the intensity of agricultural carbon emissions changed considerably, with an overall decreasing trend, in which about half of the counties (cities) were in the lower intensity zone. ③ The spatial class distribution pattern of counties (cities) in Fujian Province from 2001 to 2020 had 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 was alleviated. [Conclusion] During 2001—2020, most counties in Fujian Province have showed a decreasing trend in agricultural carbon emissions and carbon emission intensity, and carbon emission reduction has achieved certain results, but the decline has not been large enough. In the future, policy incentives and measures should be taken to optimize industrial structure, therefore to strengthen emission reductions and to promote the transition to low-carbon agriculture.