Economic growth is accompanied by the continuous increase in carbon emissions, exacerbates the severity of global warming and climate change. Analyzing the spatiotemporal characteristics of net carbon emissions and identifying their decoupling effects from economic development, along with the influencing factors, is of great practical significance for promoting regional development strategies towards low-carbon, green, and sustainable practices. Taking the Pearl River Delta Urban Agglomeration as an example, this study analyzes the carbon emissions at the municipal level and the spatiotemporal evolution of carbon sink capacity, representing the extent of net carbon emissions using the Ecological Carrying Capacity Index. Simultaneously, the Tapio decoupling model is employed to assess the decoupling index between net carbon emissions and economic effects, supplemented by the Logarithmic Mean Divisia Index (LMDI) to identify and analyze the influencing factors of the decoupling index for net carbon emissions. The results show that: (1) From 2000 to 2020, the total carbon emissions in the Pearl River Delta region exhibited a trend of rapid growth followed by a slower increase, with the emissions increasing from 1.75×10⁸ tons in 2000 to 4.87×10⁸ tons in 2020, representing a growth rate of 178.29%. (2) During the same period, the carbon absorption capacity in the Pearl River Delta region increased from 1.84×10⁸ tons to 2.06×10⁸ tons, with forests and cultivated land being the main contributors, accounting for over 97% of the total carbon absorption. (3) The carbon ecological carrying capacity index in the Pearl River Delta region exhibits significant spatial differences, showing a trend of being lower in the central areas and higher on the periphery. The peripheral areas, such as Zhaoqing, Huizhou, and Jiangmen, have a high ecological carrying capacity index. In contrast, cities like Foshan and Dongguan display a lower ecological carrying capacity index. (4) Factors such as carbon emission intensity, energy consumption, efficiency, and population have significant effects on the decoupling effect between net carbon emissions and economic development. Enhancing ecological services and increasing green space management contribute to strengthening carbon sequestration capacity, thereby promoting the decoupling of carbon emissions from economic growth. Based on these findings, the study suggests that the Pearl River Delta region should prioritize strengthening carbon sequestration capacity in its future development. Additionally, the region should adjust its industrial structure and energy mix, gradually reducing reliance on high-carbon emission industries, and promoting the decoupling of economic growth from carbon emissions. This approach is crucial for the region to address global climate change and achieve carbon neutrality goals, playing a significant strategic role in this endeavor.