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Rapid urbanization has seriously interfered with the carbon sink function of forests, and has even led to an increased risk of forest carbon imbalance. It is important to explore the regional carbon compensation mechanism and zoning optimization path based on forest carbon accounting to achieve the “dual carbon” goal and sustainable forest management in Fujian Province. Based on remote sensing and GIS technologies, this study measured forest carbon emissions and carbon sequestration of each county in Fujian Province, revealed spatial and temporal evolution of forest carbon budget during the period from 2000 to 2020, and calculated carbon compensation value of each county, so as to realize scientific accounting of forest carbon compensation, and then explored zoning optimization pathways of forest carbon compensation in Fujian Province. The results show the following: (1) From 2000 to 2020, the forest carbon budget in Fujian Province as a whole showed a spatial pattern of “coastal deficit, northwest surplus”, with obvious spatial imbalance characteristics, and showed a high growth trend of net carbon sequestration. (2) From 2000 to 2020, the average carbon compensation rate in Fujian Province was 7.92, and compensation zones were mainly concentrated in the economically developed southeast coastal regins such as Fuzhou, Quanzhou, Xiamen, Zhangzhou, and Putian, while compensation-receiving zones were mainly concentrated in northwestern mountainous areas such as Nanping, Ningde, and Longyan, which had a high forest coverage rate. (3) From 2000 to 2020, there was a significant difference in growth rates of compensation amounts and compensation-receiving amounts in Fujian Province. The cumulative increase in compensation amounts was 322.82%, while the cumulative increase in compensation-receiving amounts was only 17.5%. (4) Based on priority levels, the counties in Fujian Province are classified into six types of forest carbon compensation zones—potential compensation zones, secondary compensation zones, priority compensation zones, potential compensation-receiving zones, secondary compensation-receiving zones and priority compensation-receiving zones—and optimization paths of differentiated zones are explored.