Observing spatial inequities in carbon dynamics at fine scales is critical for formulating precise zoning policies and emission reduction strategies. However, existing research has paid limited attention to the long-term spatiotemporal evolution of carbon budgets at fine scales, often overlooking comparative differences in natural resource endowments and socio-economic conditions across regions. To address this gap, we developed a "carbon source- carbon sequestration " quantification model using multi-source data and employed a hierarchical analysis approach to examine carbon budget inequities in the Yangtze River Delta (YRD) region at both grid and county scales. A multidimensional evaluation system was constructed to elucidate the interactions among key indicators, and compensation zoning types were refined based on functional zone positioning. The results reveal that: (1) At the grid scale, carbon emissions transitioned from point-like to patchy agglomeration, while carbon sequestration expanded outward from major mountain ranges, forming multi-scale sequestration surfaces. At the county scale, carbon emissions exhibited a "core-periphery" structure, with carbon sequestration showing a "high in the south, low in the north" spatial heterogeneity. (2) The carbon budget characteristics of functional zones aligned with their designated roles, with greater variability in the concentration index of carbon emissions compared to sequestration. (3) Scale background attributes (SBA) and socio-economic attributes (SEA) exhibited a nonlinear negative correlation, while spatial structure attributes (SSA) positively influenced ecological environment attributes (EEA), particularly in Optimized Development Zones (ODZ). (4) Based on the spatial comparative advantages of attribute indicators, 120 payment zones, 95 balancing zones, and 90 compensation zones were identified, further refined into 10 distinct carbon compensation zoning types integrated with major functional zones. This study provides a more equitable framework for cross-regional carbon compensation through fine-scale analysis and functional zone perspectives, offering scientific support for collaborative emission reduction efforts.