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• The method of compiling the multi-regional input output is optimized. • Carbon emissions of urban agglomerations (UAs) are studied from multiple perspectives. • Carbon flows within the UA driven by final demand and primary inputs are identified. • Carbon emissions of the UA are predicted when considering uncertainty. Urban agglomerations (UAs) play a momentous role in carbon reduction. The prerequisites for achieving carbon reduction goals in UAs are accounting and predicting their carbon emissions. When considering carbon reduction goals in China, it is crucial to pay attention to the joint influence of carbon emissions and economic benefits. Hence, in this study, an improved multi-regional input–output (MRIO) approach was established to quantify and predict carbon emissions for the UA, incorporating a biproportional scaling method (RAS) and Latin hypercube sampling (LHS). Specifically, a) the carbon emissions of UAs were quantified using the MRIO model from the perspectives of production, consumption and income; b) the carbon flows between cities in UAs were identified based on final demand and primary inputs, and c) the features of UAs' carbon emissions in the future were predicted using RAS and LHS. To verify the effectiveness of the approach, a case study of a typical UA region in China [i.e., the Pearl River Delta (PRD)] was proposed. The results showed that the contribution of sectors to carbon emissions could be identified from multiple perspectives, and carbon flows can help regions coordinate emissions reductions. The majority of future carbon emissions would be generated from the areas of population and economic agglomeration (i.e., Guangzhou and Shenzhen), although the growth trend of carbon emissions of those would keep lower. The policy of carbon reduction should be urgently carried out in locations with high carbon emissions growth rates (e.g., Zhaoqing and Zhuhai). To improve the ability for carbon reduction in the PRD, cooperation in multiple cities to promote energy efficiency is advocated. The government should also increase technical support for carbon reduction and consider the balanced development of the economy, population, and resources in the PRD. [ABSTRACT FROM AUTHOR]