The precise acquisition of phenotypic parameters for individual trees in plantation forests is important for forest management and resource exploration. The use of Light-Detection and Ranging (LiDAR) technology mounted on Unmanned Aerial Vehicles (UAVs) has become a critical method for forest resource monitoring. Achieving the accurate segmentation of individual tree crowns (ITCs) from UAV LiDAR data remains a significant technical challenge, especially in broad-leaved plantations such as rubber plantations. In this study, we designed an individual tree segmentation framework applicable to dense rubber plantations with complex canopy structures. First, the feature extraction module of PointNet++ was enhanced to precisely extract understory branches. Then, a graph-based segmentation algorithm focusing on the extracted branch and trunk points was designed to segment the point cloud of the rubber plantation. During the segmentation process, a directed acyclic graph is constructed using components generated through grey image clustering in the forest. The edge weights in this graph are determined according to scores calculated using the topologies and heights of the components. Subsequently, ITC segmentation is performed by trimming the edges of the graph to obtain multiple subgraphs representing individual trees. Four different plots were selected to validate the effectiveness of our method, and the widths obtained from our segmented ITCs were compared with the field measurement. As results, the improved PointNet++ achieved an average recall of 94.6% for tree trunk detection, along with an average precision of 96.2%. The accuracy of tree-crown segmentation in the four plots achieved maximal and minimal R² values of 98.2% and 92.5%, respectively. Further comparative analysis revealed that our method outperforms traditional methods in terms of segmentation accuracy, even in rubber plantations characterized by dense canopies with indistinct boundaries. Thus, our algorithm exhibits great potential for the accurate segmentation of rubber trees, facilitating the acquisition of structural information critical to rubber plantation management.