In order to study the survival status and distribution pattern of Dacrydium pectinatum population, we investigated three different distribution areas, namely BWL, DLS, and JFL in Hainan Island. The spatial heterogeneity in three aspects of the species diversity and dominant species composition of the natural community arbor layer, age structure, and distribution pattern was analyzed. The results showed that (1) the arbor layer species abundance and diversity index of the three D. pectinatum natural community were higher as a whole, which followed the order of BWL > JFL > DLS, and much higher than those of the mid-high latitude temperate zone and subtropical forest community. The populations in the community were mostly small-density populations, and there were few absolutely dominant species, which is consistent with the general rule of species composition of tropical mountain rainforests. (2) The age structure of these three populations had its own characteristics. BWL and JFL showed a recession trend. The common feature was that the number of Juvenile tree was small, and the proportion of adult trees and elderly trees was high. The number of Juvenile tree in DLS was the most for all individuals and belonged to the growth population. (3) The overall state of the D. pectinatum population of BWL and JFL was aggregate clustered distribution. The juvenile tree stage was also a clustered distribution, but in the elderly tree stage, it changed from clustered distribution to uniform distribution. The JFL D. pectinatum population showed a uniform distribution throughout all individuals and different developmental stages. Their aggregation intensity was expressed as DLS > BWL > JFL and juvenile > adult > elderly. D. pectinatum is a key species of tropical mountain rainforests, which is of great significance for studying the origin and flora characteristics of Hainan tropical rainforest. For its current survival status, we can use manual auxiliary measures such as opening forest windows and rational thinning to protect and rejuvenate D. pectinatum population based on the actual situation.