In this paper, a method of recognizing the trunk point cloud of natural forest trees in the mining area using a hand-held laser scanner is proposed in order to quantitatively describe the three-dimensional structure information of natural forest trees in complex environment of the mining area. The natural forest in the mining area is scanned with a hand-held laser scanner. On the basis of filtering the ground points, the multi-scale verticality feature is introduced to identify the trunk of the natural forest in the mining area, and the identified trunk is further extracted by the octree leaf node clustering method. Experiments are carried out with measured data from the mining area, and the results show that the proposed method can realize the identification of the trunk of natural forest in the mining area, and has certain reference value for quantitative description of the three-dimensional structure information of natural forest trees in complex environment, and for clarifying the vegetation growth status in the mining area.