Three well-conserved Horsfieldia hainanensis Merr. populations were used to investigate their soil seed bank and seedling regeneration characteristics and their relationship to environmental factors. The results showed that the seed reserves were low in the H. hainanensis soil seed bank (16.93~24.74 seed/m2). The distribution pattern for the seeds and seedlings in the H. hainanensis populations was aggregated, and they were mainly found around 2–3 m from the mother plant. The seeds in the litter layer and the 5–10 cm soil layer showed no vigor, and only 25.7%~33.3% of the total seeds in the 0–5 cm soil layer were viable affected by the high temperature and humidity, the animals’ eating and poisoning. Affected by the height and coverage of the surrounding herbaceous layer and shrub layer, the seedlings of H. hainanensis could not obtain enough light and nutrients in the competition, resulting in the survival competitiveness of 1- to 3-year-old (1–3a) seedlings in the habitat had been in a weak position and a large number of seedlings died. It would take at least four years for seedlings to develop under the current environmental constraints. It can be concluded that the low seed reserve in the soil seed bank and high mortality of seedlings of H. hainanensis lead to slow or even stagnation of population regeneration, which was an important reason for the endangered of H. hainanensis. Therefore, the next research focus is to explore the influence mechanism of environmental factors on seed germination and seedling growth of H. hainanensis.