Mangrove forests have unique ecosystem functions and services, yet the coastal mangroves in tropics are often disturbed by tropical cyclones. Hurricane Maria swept Puerto Rico and nearby Caribbean islands in September 2017 and caused tremendous damage to the coastal mangrove systems. Understanding the vulnerability and resistance of mangrove forests to disturbances is pivotal for future restoration and conservation. In this study, we used LiDAR point clouds to derive the canopy height of five major mangrove forests, including true mangroves and mangrove associates, along the coast of Puerto Rico before and after the hurricanes, which allowed us to detect the spatial variations of canopy height reduction. We then spatially regressed the pre-hurricane canopy height and the canopy height reduction on biophysical factors such as the elevation, the distance to rivers/canals within and nearby, the distance to coast, tree density, and canopy unevenness. The analyses resulted in the following findings. The pre-hurricane canopy height increased with elevation when elevation was low and moderate but decreased with elevation when elevation was high. The canopy height reduction increased quadratically with the pre-hurricane canopy height, but decreased with elevation for the four sites dominated by true mangroves. The site of Palma del Mar dominated by Pterocarpus, a mangrove associate, experienced the strongest wind, and the canopy height reduction increased with elevation. The canopy height reduction decreased with the distance to rivers/canals only for sites with low to moderate mean elevation of 0.36–0.39 m. In addition to the hurricane winds, the rainfall during hurricanes is an important factor causing canopy damage by inundating the aerial roots. In summary, the pre-hurricane canopy structures, physical environment, and external forces brought by hurricanes interplayed to affect the vulnerability of coastal mangroves to major hurricanes.