Urban expansion has an impact on the carbon sequestration capacity of terrestrial ecosystems through alterations in gross primary productivity (GPP), which can have implications for ecosystem functioning and regional carbon budgets. Urban expansion leads to the transformation of vegetation into impervious water, resulting in the reduction of vegetation cover, which in turn leads to the reduction of GPP. However, the change of regional climate caused by urbanization will affect vegetation growth, and vegetation productivity also changes with time under the background of climate change. Based on multi-source remote sensing data and downscaled vegetation productivity data, this study examines the spatiotemporal dynamics of urban expansion, its direct and indirect impacts on gross primary productivity (GPP) in Nanjing from 2000 to 2020, and the compensation proportion of the indirect effects of urbanization and climate change for direct effects. The findings indicate a significant expansion of the urban area in Nanjing between 2000 and 2020, resulting in the double of impervious surface from 620.31 km2 in 2000 to 1245.66 km2 in 2020. Due to the increase of urbanization intensity, the direct effect of land cover change resulted in a decrease of -345.98 gC/m2/a in the GPP of Nanjing urban area, while the indirect effect of regional climate change and urbanization resulted in an increase of 298.67 gC/m2/a in the GPP of Nanjing urban area, which offset 86.33% of the direct effect. The increasing trend and contribution rate of indirect influences in urban areas surpass those in suburban areas, demonstrating that the urban environment fosters residual vegetation growth. In the context of the continuous expansion of major cities worldwide, characterizing and understanding the impact of urban expansion on vegetation productivity holds significant practical significance and reference value in addressing global change challenges and promoting ecologically civilized city construction.