Climate changes and human-mediated modifications to ecosystems have threatened the biodiversity and habitats of various species. Dacrydium pectinatum is a constructive and endangered species in the tropical mountain forests of Hainan Island, China. In this study, we established sixty-eight 30 m × 30 m permanent plots of D. pectinatum along an environmental axis of temperature and precipitation in the west (Bawangling, 30 plots), southwest (Jianfengling, 30 plots) and east (Diaoluoshan, 8 plots) of Hainan Island. Our objectives are to explore the change mechanisms of plant composition/diversity in the D. pectinatum community at distinct environmental scales and analyze the association between environmental factors (topography, soil and stand conditions) and vegetation distribution. The results showed that the diversity of D. pectinatum communities was lower than that in tropical forests at other sites around the world and much higher than that in subtropical forests at similar latitudes. At the regional scale, plant diversity showed a pattern that decreases with increasing latitude; at the local scale, diversity decreases with increasing elevation. Eight environmental factors, namely, elevation, slope, canopy density, soil organic matter, soil pH, soil total nitrogen, soil available phosphorus and soil available potassium, showed a significant correlation to species distribution. Elevation factors were identified as the determinants of the overall diversity patterns. In conclusion, our study clarified that abiotic environmental factors strongly influence the vegetation structure and diversity pattern of the D. pectinatum communities in various environmental scales. Low temperatures, high humidity, low soil nutrients, and high stand density may be the limiting factors that cause their diversity to decline. We recommend various actions to ameliorate the impact of environmental changes on the D. pectinatum community, such as protecting existing habitats, strengthening monitoring of restrictive environmental factors, appropriate thinning of higher density stands, and conducting research on genetic diversity to improve the community survivability.