LiDAR-unmanned aerial system (LiDAR-UAS) technology can accurately and efficiently obtain detailed and accurate three-dimensional spatial information of objects. The classification of objects in estuarine areas is highly important for management, planning, and ecosystem protection. Owing to the presence of slopes in estuarine areas, distinguishing between dense vegetation (lawns and trees) on slopes and the ground at the tops of slopes is difficult. In addition, the imbalance in the number of point clouds also poses a challenge for accurate classification directly from point cloud data. A multifeature-assisted and multilayer fused neural network (MLF-PointNet++) is proposed for LiDAR-UAS point cloud classification in estuarine areas. First, the 3D shape features that characterize the geometric characteristics of targets and the visible-band difference vegetation index (VDVI) that can characterize vegetation distribution are used as auxiliary features to enhance the distinguishability of dense vegetation (lawns and trees) on slopes and the ground at the tops of slopes. Second, to enhance the extraction of target spatial information and contextual relationships, the feature vectors output by different layers of set abstraction in the PointNet++ model are fused to form a combined feature vector that integrates low and high-level information. Finally, the focal loss function is adopted as the loss function in the MLF-PointNet++ model to reduce the effect of imbalance in the number of point clouds in each category on the classification accuracy. A classification evaluation was conducted using LiDAR-UAS data from the Moshui River estuarine area in Qingdao, China. The experimental results revealed that MLF-PointNet++ had an overall accuracy (OA), mean intersection over union (mIOU), kappa coefficient, precision, recall, and F1-score of 0.976, 0.913, 0.960, 0.953, 0.953, and 0.953, respectively, for object classification in the three representative areas, which were better than the corresponding values for the classification methods of random forest, BP neural network, Naive Bayes, PointNet, PointNet++, and RandLA-Net. The study results provide effective methodological support for the classification of objects in estuarine areas and offer a scientific basis for the sustainable development of these areas.