High-resolution UAV imagery paired with a convolutional neural network approach offers significant advantages in accurately measuring forestry ecosystems. Despite numerous studies existing for individual tree crown delineation, species classification, and quantity detection, the comprehensive situation in performing the above tasks simultaneously has rarely been explored, especially in mixed forests. In this study, we propose a new method for individual tree segmentation and identification based on the improved Mask R-CNN. For the optimized network, the fusion type in the feature pyramid network is modified from down-top to top-down to shorten the feature acquisition path among the different levels. Meanwhile, a boundary-weighted loss module is introduced to the cross-entropy loss function Lmask to refine the target loss. All geometric parameters (contour, the center of gravity and area) associated with canopies ultimately are extracted from the mask by a boundary segmentation algorithm. The results showed that F1-score and mAP for coniferous species were higher than 90%, and that of broadleaf species were located between 75%–85.44%. The producer’s accuracy of coniferous forests was distributed between 0.8–0.95 and that of broadleaf ranged in 0.87–0.93; user’s accuracy of coniferous was distributed between 0.81–0.84 and that of broadleaf ranged in 0.71–0.76. The total number of trees predicted was 50,041 for the entire study area, with an overall error of 5.11%. The method under study is compared with other networks including U-net and YOLOv3. Results in this study show that the improved Mask R-CNN has more advantages in broadleaf canopy segmentation and number detection.