Increasing human activities have caused serious disturbance to global forest resources, so how to accurately identify individual trees has become an important task of forest resources investigation. In order to get the accurate number of individual trees, this paper took coniferous forest and mixed coniferous and broad-leaved forest as experimental samples, as well as Digital Orthophoto Map and airborne LiDAR Point Cloud as research data. We propose a deep Learning individual tree segmentation method based on RetinaNet model and PCS algorithm by doing comparative analysis (classical Watershed Algorithm and Layer Stacking Algorithm) at the plots (with high, medium, and low densities). The experimental results show that the method proposed in this paper can solve the problem of individual tree segmentation in high density forest and improve its degree of automation. Compared with Watershed algorithm and Layer stacking algorithm, F-Measure is improved by 6%-29% and 7%-20%, respectively. In other words, the results of individual tree segmentation presented in this paper can not only improve the precision of individual tree segmentation, but also maintain a high detection rate, which can meet the accuracy and high efficiency of individual tree extraction, so as to meet the needs for modern forestry investigation.