Nowadays, the 3D individual tree reconstruction has played a significant role in the phenotypic study of trees. This paper proposes a new automatic method for extracting skeletons of individual trees and reconstructing 3D models. Firstly, the Euclidean clustering is performed to obtain center points of candidate branch regions. Then, the initial skeletons of LiDAR point clouds are obtained by slicing clusters in three dimensions. Secondly, skeleton points are completed by the proposed branch tracking. Then, the radius of the branches is accurately estimated from the branches. Thirdly, optimal points are interpolated in appropriate directions to refine skeletons of individual trees. Then, the Laplacian algorithm is conducted for smoothing branches. After that, optimal geometric shapes are formulated to reconstruct the final 3D tree models. Experimental results show that the average accuracy of our individual tree models is up to 97.49%, which shows a promising algorithm in 3D tree reconstructions.