Scyphiphora hydrophyllacea is an endangered mangrove species in China. Over-exploitation and coastal development have drastically reduced its distribution and population, now limited to the Qingmei Port (Sanya) and the Qinglan Port (Wenchang). Despite its critical status, research on its ecological roles remains limited. This study examines the characteristics of S. hydrophyllacea communities and their relationship with soil properties. A total of 17 species from 11 families and 14 genera were recorded. TWINSPAN classification identified two distinct community types: the Qinglan Port community and the Qingmei Port community. Significant biodiversity differences were found only in the tree layer, with no differences in shrub or herbaceous layers. The importance value of S. hydrophyllacea within the arbor layer exhibited variability across the two communities, serving as an associated species in the Qinglan Port community and as a dominant species in the Qingmei Port community, suggesting potential barriers to its natural regeneration. Redundancy analysis (RDA) revealed that key soil factors influencing S. hydrophyllacea’s distribution include electrical conductivity (EC), total phosphorus (TP), total nitrogen (TN), soil organic content (SOC), and carbon/nitrogen ratio (C/N). We propose that high soil salinity and nitrogen deficiency may act as key factors limiting the natural regeneration of S. hydrophyllacea.