Rapid urbanization has a significant impact on the ecological environment. Net primary productivity (NPP) can effectively reflect the growth of urban vegetation and the carbon sequestration capacity of an ecosystem. Taking the rapidly growing Pearl River Delta (PRD) as our study area, the relative contributions of human activities and climate change to NPP were analyzed using an improved two-step method based on residual trend analysis. The decoupling index was used to compare the coordinated development of socioeconomic factors and the NPP in different time periods. This study lays the foundation for formulating comprehensive and reasonable urban low-carbon development measures. The results showed that (1) NPP decreased significantly before 2010, but by 2019, NPP in most regions of the PRD showed a slight increase. The NPP of new urban land was better than that of original urban land. (2) The negative contribution of climatic factors to NPP was clearer than that of human activities, and human activities contributed positively to NPP outside urban land. (3) The decoupling status of socioeconomic factors and NPP is improving, and the degree of decoupling in 2010–2019 was higher than that in 2000–2010. In conclusion, as the first forest urban agglomeration in China, the PRD has shown a good implementation of carbon sequestration policies, which can provide a reference for the coordinated development of urbanization and carbon sequestration.