The increase in environmental and human-related changes (e.g., increase in the carbon cycle flux of plants) has increased the dynamism of ecosystems. Examining fluctuations in net primary production (NPP) is very important in adopting correct strategies for ecosystem management. The current study explores the spatiotemporal variations in NPP and its association with agricultural droughts in Iran’s ecosystems over 20 years (2000–2020). Mann–Kendall and Sen’s slope methods in each pixel were used to track changes in trends. Drought upsets the terrestrial carbon cycle balance. In this study, Vegetation Health Index (VHI) used to assess drought that extracted from different bands of images satellite. Then, the relationship between NPP rates and agricultural droughts was investigated through running Pearson correlation. The results demonstrated that Iran’s annual share of carbon sequestration is 1.38 kg*C/m2/year. The highest carbon sequestration rate was recorded in Caspian Hyrcanian forests. In contrast, the lowest rate was observed in the Arabian Desert and East Sahero-Arabian xeric shrublands in southwestern Iran. Moreover, the highest photosynthesis variations were recorded in Arabian Desert and East Sahero-Arabian xeric shrublands and Tigris–Euphrates alluvial salt marsh, while the lowest changes were registered in Badghyz and Karabil. In total, 34.2% of the studied pixels showed a statistically significant rising or falling trend. Sen’s slope estimator demonstrated that the sharpest negative trend in carbon sequestration belonged to Caspian Hyrcanian mixed forests (−12.24 g*C/m2/year), while the sharpest positive trend was observed in Azerbaijan shrub desert and steppe (12.29 g*C/m2/year). The results of the Pearson correlation revealed significant correlations between NPP and VHI in different ecosystems with coefficients ranging from −0.93 to 0.95. The largest area with a positive correlation (33.97%) belonged to the Zagros Mountains forest steppe. Identification of areas with the greatest carbon sequestration changes could result in prioritizing varied ecosystems management for carbon sequestering. It can be also utilized in environmental planning such as scaling up ecosystem values or estimating current and past ecological capacity.

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