Historic gardens contain a greater number and variety of ancient trees, which are older, have unique forms, and larger volumes. These trees hold significant value in both natural ecosystems and cultural heritage. However, current research on the carbon sequestration value of ancient and non-ancient trees in historical gardens is relatively lacking. Based on the unique morphology and carbon storage estimation needs of ancient trees in historic gardens, this paper proposes a morphology-based point cloud single-tree segmentation method. This method can precisely extract the morphological structures of various tree species and accurately estimate their carbon storage. From the perspective of carbon sequestration, it evaluates the correlation between the structural characteristics and carbon storage of trees in historic gardens, as well as the potential changes in their carbon storage capacity.Using the Jing Yi Park’s Jian Xin Pavilions in Fragrant Hills Park as a case study, this method was applied to extract structural indicators of 116 ancient and non-ancient trees. The total carbon storage was found to be 19,171.13 kg, with an average carbon storage of 165.27 kg per tree. Among these, ancient trees accounted for 13,178.32 kg, or 68.74% of the total carbon storage. The study revealed that the correlation between tree age and carbon storage varied by species, and there were significant positive correlations between carbon storage and tree height, DBH, and canopy volume. Notably, there was a significant linear growth trend between DBH, canopy volume, and carbon storage. By 2030, the total carbon storage is projected to increase to 21,924.96 kg, with an annual average increase of 393.40 kg, representing a growth rate of 14.4%.The results indicate that studying the correlation between structural characteristics and carbon storage of aged trees in historical gardens can shed light on the important role of trees in sustainable carbon sequestration. The precise extraction of tree information through 3D digital technology and the prediction of carbon storage potential not only offer new perspectives for the conservation of cultural heritage in historical gardens, urban microclimate planning and design, and spatial management of carbon sinks and emissions but also have significant value for promoting the scientific management and protection of urban green spaces.