Forest ecosystems are vital for climate mitigation, yet predicting their carbon (C) sequestration remains challenging, especially in urban-proximal regions. This study investigates the C storage dynamics across five major forest types in the Chang-Zhu-Tan Green Heart, a critical ecological buffer zone in China’s Yangtze River Mid-Reach urban agglomeration. We integrated field measurements with structural equation and random forest modeling to analyze vertical C distribution and its drivers. The results revealed that over 90% of vegetation C was stored in the tree layer, with soil C highest in evergreen broad-leaved forests (41.26 Mg C/ha). Biological factors (i.e., tree volume and biomass) primarily drove vegetation C (52–73% of variance), while non-biological factors (soil properties and micronutrients) predominantly regulated soil C. We identified distinct age-related trajectories: J-shaped accumulation in broad-leaved forests versus S-shaped patterns in coniferous and mixed forests. These findings provide a mechanistic framework for forest-type-specific management strategies to enhance C sequestration in urban-agglomeration buffer zones.