In the Hainan Tropical Rainforest National Park, established in 2021, certain vegetation areas have been subjected to anthropogenic disturbance due to historical causes. This study examines the tropical rainforest sections in three sub-regions within the park, namely Bawangling, Diaoluoshan, and Jianfengling, and investigates the effects of varying degrees of long-term disturbance on species richness, diversity, composition, as well as the combined impact of topographic and biological factors using the spatio-temporal substitution method. The results indicated that long-term disturbance reduced the α-diversity, while increasing β-diversity. Similarities in species composition decreased along the gradient of long-term disturbance. There was a negative correlation between long-term disturbance and woody plant species composition. Long-term disturbance diminished the relationship between the richness of woody plants and both topographic and biological factors, directly affecting the abundance of these plants. To maintain the biodiversity of the Hainan National Park, it is crucial to focus on monitoring forest communities that are severely disturbed within the park.