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Net Primary Productivity (NPP) can effectively reflect the characteristics and strength of the response to external disturbances on estuarine alluvial island ecosystems, which can provide evidence for regulating human development and utilization activities and improving blue carbon capacity. However, there are a few studies on NPP of estuarine alluvial islands. We established a model based on a Carnegie–Ames–Stanford Approach (CASA) to estimate NPP on Chongming Island, a typical estuarine alluvial island, by considering the actual ecological characteristics of the island. The NPP of different land-cover types and protected areas in different years and seasons were estimated using Remote Sensing and Geographic Information System as the main tools. Correlations between NPP and Remote Sensing-based spatially heterogeneous factors were then conducted. In the last 30 years, the mean NPP of Chongming Island initially increased and then slowly decreased, while total NPP gradually increased. In 2016–2017, Chongming Island total NPP was 422.32 Gg C·a−1, and mean NPP was 287.84 g C·m−2·a−1, showing significant seasonal differences. NPP showed obvious spatial differentiation in both land-cover and protected area types, resulting from joint influences of natural and human activities. Chongming Island vegetation growth status and cover were the main factors that positively affected NPP. Soil surface humidity increased NPP, while soil salinity, surface temperature, and surface aridity were important NPP limiting factors.
