In order to reconstruct high-quality 3D tree models, trunks and crowns could be reconstructed using appropriate methods separately and merged together. During this process, gaps will appear after tree models are spliced, which will affect the models' topological connectivity and visual effects. In this paper, a gap-repair algorithm for tree mesh models based on boundary restriction and coordinates projection is proposed. The algorithm first extracts all the holes in the tree trunk meshes and crown meshes and matched them according to their relative positions. Then, the gaps in the tree meshes are identified. After that, based on the projection of the hole vertices from 3D space to 2D space, the relative positions of the hole vertices were determined, and vertex connection and surface addition were carried out to generate a 2-manifold patch. Finally, the patch was refined to keep its density of vertices similar to the surrounding meshes. Real 3D Tree meshes of different species were used to conduct experiments, and the quality of the repaired tree models are evaluated qualitatively and quantitatively. Experimental results revealed that the proposed algorithm could fill gaps in tree meshes quickly and effectively, so as to achieve the topology connection and smooth transition between the trunk and crown meshes.