Compared with ground-based light detection and ranging (LiDAR) data, the differential distribution of the quantity and quality of point cloud data from airborne LiDAR poses difficulties for tree species classification. To verify the feasibility of using the PointNet++ algorithm for point cloud tree species classification with airborne LiDAR data, we selected 11 tree species from the Minjiang River Estuary Wetland Park in Fuzhou City and Sanjiangkou Ecological Park. Training and testing sets were constructed through pre-processing and segmentation, and direct and enhanced down-sampling methods were used for tree species classification. Experiments were conducted to adjust the hyperparameters of the proposed algorithm. The optimal hyperparameter settings used the multi-scale sampling and grouping (MSG) method, down-sampling of the point cloud to 2048 points after enhancement, and a batch size of 16, which resulted in 91.82% classification accuracy. PointNet++ could be used for tree species classification using airborne LiDAR data with an insignificant impact on point cloud quality. Considering the differential distribution of the point cloud quantity, enhanced down-sampling yields improved the classification results compared to direct down-sampling. The MSG classification method outperformed the simplified sampling and grouping classification method, and the number of epochs and batch size did not impact the results.