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The previous literatures have insufficient content on spatial dependence and heterogeneity of agricultural carbon emissions (ACEs), which is inconsistent with the actual situation, weakening the practical significance of research conclusions. To fill this knowledge gap, this study attempts to explore the spatial evolution pattern of ACEs at the city-scale in the Fujian Province of China from spatio-temporal latitudes and adopts the exploratory spatial data analysis method (ESDA) to analyze the spatial correlation effects of ACEs. The findings revealed that ACEs in Fujian show a downtrend as a whole. From the perspective of carbon sources of ACEs, agricultural materials and livestock breeding caused the largest emissions, accounting for 73.82% of the total ACEs, while rice growth led to the smallest carbon emissions, accounting for 26.18% of the total ACEs. We also found that there is obvious non-equilibrium in the spatial distribution of ACEs and their intensity, showing a strong spatial correlation; and although a relatively obvious clustering area has been formed, the spatial autocorrelation of most regions is not significant. Accordingly, we suggest that exploring the “carbon compensation mechanism”, is conducive to stimulating the low-carbon agricultural production behavior with positive externalities, to reduce agricultural carbon emissions.