Accurate individual tree reconstruction based on laser point clouds is vital for precise biomass estimation, virtual geographic environment modeling, and simulation. However, mobile laser 3D scanning systems often capture tree point clouds obscured by leaves, resulting in missing or incomplete branch data, posing significant challenges to detailed tree reconstruction. In this paper, a novel method for fine-grained 3D tree model reconstruction from incomplete point clouds is proposed. This approach addresses the structural reconstruction of trees, tackling two main problems: reconstructing the main trunk and branches based on data completeness. Initially, a 3D morphological algorithm is employed to separate the main trunk and branches in the point cloud. Next, branch point clouds are node-aggregated using clustering, and the trunk’s skeleton point is computed using a multi-scale curve fitting method. To account for incomplete branch point clouds, the Alpha shape is calculated and used as a constraint for the growth model of the L-system, enabling the automatic generation of branch structures. Finally, a morphologically constrained multi-level trunk fusion method is utilized to achieve complete tree model reconstruction. To validate the effectiveness of this method, five trees with varying structures and levels of complexity were selected for structural reconstruction and compared with state-of-the-art (SOTA) methods. Experimental results evince that the method delineated in this study exhibits an aptitude for adeptly approximating tree nodes, even in scenarios characterized by incomplete point cloud data. This approach transcends the reconstruction accuracy manifested by SOTA algorithms specific to three-dimensional tree modeling, simultaneously demonstrating a pronounced resilience to noise and enhanced robustness.