As China’s largest cross-regional urban agglomerations, the middle reaches of the Yangtze River urban agglomerations (MRYRUA) possess both significant societal carbon source volume and ecological carbon sequestration capacity. Nevertheless, with the uncontrolled expansion of urban energy consumption activities and the industry migration from eastern coastal regions to inland cities, the carbon budget pattern of territorial space is increasingly unbalanced in the MRYRUA. To achieve low-carbon regulation, this study utilized land use and energy consumption data from 31 cities within the MRYRUA to establish a “carbon source-carbon sink” quantification and spatiotemporal exploration model, revealing the spatial-temporal variation of carbon budgets from 2005 to 2020. Furthermore, we developed a carbon balance indicator analysis system by employing the carbon offset rate (COR), carbon productivity (CP), Gini coefficient, ecological support coefficient (ESC), economic contribution coefficient (ECC), and functional zoning was performed. Finally, using the GM (1,1) model, we derived the carbon budget pattern for 2050 and explored the differentiated regulatory mechanisms under the carbon balance perspective. The results indicated that: (1) The MRYRUA’s territorial carbon budgets have increased annually, displaying a spatial distribution pattern with the highest values in the central region, followed by the northwest, and the lowest in the southeast near water bodies. The spatiotemporal differentiation effects manifest as an east–west axial development trend, with spatiotemporal clustering effects demonstrating a propensity for outward dispersion from the northern hot spot radiation core. (2) The MRYRUA’s COR has consistently remained below 10% and decreased annually, while the CP has shown a yearly increase at an accelerating rate. The ESC and ECC exhibit evident spatial heterogeneity among cities. In response to the carbon emission economic benefits and carbon sequestration ecological carrying capacity reflected by carbon balance indicators, each city was classified into low-carbon economic zones, carbon intensity control zones, carbon sink functional zones, and high-carbon optimization zones. (3) From 2020 to 2050, the polarization trend of the carbon budget pattern continues to intensify. Subsequently, we have established a differentiated territorial spatial carbon balance regulatory mechanism. This mechanism strengthens the leading role of low-carbon economic zones in the green low-carbon transition, moderately retains the carbon sink functional zones in the southeast with solid carbon fixation capabilities, and promotes the transition of the northern carbon intensity control zones and high-carbon optimization zones to low-carbon economic zones. The research findings provide a scientific basis for formulating territorial spatial planning policies from a carbon neutrality perspective.
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