Quantitatively characterizing coastal salt-marsh terrains and the corresponding spatiotemporal changes are crucial for formulating comprehensive management plans and clarifying the dynamic carbon evolution. Multiline light detection and ranging (LiDAR) exhibits great capability for terrain measuring for salt marshes with strong penetration performance and a new scanning mode. The prerequisite to obtaining the high-precision terrain requires accurate filtering of the salt-marsh vegetation points from the ground/mudflat ones in the multiline LiDAR data. In this study, a new alternative salt-marsh vegetation point-cloud filtering method is proposed for drone multiline LiDAR based on the extreme gradient boosting (i.e., XGBoost) model. According to the basic principle that vegetation and the ground exhibit different geometric and radiometric characteristics, the XGBoost is constructed to model the relationships of point categories with a series of selected basic geometric and radiometric metrics (i.e., distance, scan angle, elevation, normal vectors, and intensity), where absent instantaneous scan geometry (i.e., distance and scan angle) for each point is accurately estimated according to the scanning principles and point-cloud spatial distribution characteristics of drone multiline LiDAR. Based on the constructed model, the combination of the selected features can accurately and intelligently predict the category of each point. The proposed method is tested in a coastal salt marsh in Shanghai, China by a drone 16-line LiDAR system. The results demonstrate that the averaged AUC and G-mean values of the proposed method are 0.9111 and 0.9063, respectively. The proposed method exhibits enhanced applicability and versatility and outperforms the traditional and other machine-learning methods in different areas with varying topography and vegetation-growth status, which shows promising potential for point-cloud filtering and classification, particularly in extreme environments where the terrains, land covers, and point-cloud distributions are highly complicated.