Effective classification of wood and leaf points from terrestrial laser scanning (TLS) point clouds is critical for analyzing and estimating forest attributes such as diameter at breast height (DBH), above-ground biomass (AGB), and wood volume. To address this, we introduce the Wood–Leaf Classification Network (WLC-Net), a deep learning model derived from PointNet++, designed to differentiate between wood and leaf points within tree point clouds. WLC-Net enhances classification accuracy, completeness, and speed by incorporating linearity as an inherent feature, refining the input–output framework, and optimizing the centroid sampling technique. We trained and evaluated WLC-Net using datasets from three distinct tree species, totaling 102 individual tree point clouds, and compared its performance against five existing methods including PointNet++, DGCNN, Krishna Moorthy’s method, LeWoS, and Sun’s method. WLC-Net achieved superior classification accuracy, with overall accuracy (OA) scores of 0.9778, 0.9712, and 0.9508; the mean Intersection over Union (mIoU) scores of 0.9761, 0.9693, and 0.9141; and F1-scores of 0.8628, 0.7938, and 0.9019, respectively. The model also demonstrated high efficiency, processing an average of 102.74 s per million points. WLC-Net has demonstrated notable advantages in wood–leaf classification, including significantly enhanced classification accuracy, improved processing efficiency, and robust applicability across diverse tree species. These improvements stem from its innovative integration of linearity in the model architecture, refined input–output framework, and optimized centroid sampling technique. In addition, WLC-Net also exhibits strong applicability across various tree point clouds and holds promise for further optimization.