Plant patches play a crucial role in understanding the biogeomorphology of saltmarshes. Although two-dimensional optical remote sensing has long been applied to the study of saltmarsh plant patches, studies focusing on the canopy features at a patch-scale remain limited. Therefore, a simple and efficient method is needed to capture three-dimensional patch features and their relationship to habitat. This study utilized UAV-based LiDAR to obtain three-dimensional patch features of the native species S. mariqueter and the invasive species S. alterniflora in Andong Shoal, Hangzhou Bay, and examine the relationship between patch distribution and geomorphological characteristics. A workflow was established to overcome the inability of low-cost LiDAR sensor to penetrate dense vegetation, resulting in no ground return. Results showed that S. alterniflora patches were smaller in size but taller in canopy height than S. mariqueter patches. Regarding morphological patterns of patch canopy, S. alterniflora exhibited single-arch patterns (29%) and double-arch patterns (16%), whereas S. mariqueter exhibited only single-arch patterns (83%). The presence of double-arch patches suggested the development of fairy circles, indicating that the invasive S. alterniflora exhibits greater ecological resilience compared to the native S. mariqueter. Furthermore, this study explored the ecological niches of the two species in the pioneer zone of Andong Shoal. The ecological niches for S. alterniflora were 2.00-2.25 m, whereas that for S. mariqueter were 1.85-2.00 m and 2.25-2.40 m. Distance from the tidal creeks significantly moderated the number and area of patches for both species. This study demonstrated that UAV-based LiDAR technology can provide high-quality three-dimensional information about the pioneer zone of saltmarsh, thus helping to understand biogeomorphological processes in this region.