Soil samples were collected from the lowland rainforest secondary forests, montane rainforest secondary forests, and montane rainforest primary forests in the Jianfengling of Hainan Island, absolute quantification PCR and high-throughput sequencing technology were used to explore the diversity and composition of carbon sequestering microbial community structure in soil and its influencing factors. The results showed that both α diversity and gene quantity of carbon-fixing microorganisms were higher in lowland rainforest secondary forest than in montane rainforest primary forest. The dominant phyla of soil carbon-fixing microorganisms in the Jianfengling rainforest were Actinomycetota (11.95%-33.73%) and Pseudomonadota (44.28%-70.60%), the dominant genera were Bradyrhizobium (11.53%-31.06%), Nocardia (4.97%-17.07%), Mesorhizobium (4.44%-12.97%), Mycobacterium (2.62%-9.20%), Blastochloris (4.34%-10.12%), Aromatoleum (1.97%-5.39%), Mycolicibacterium(1.71%-3.78%), Azospirillum (1.97%-2.65%) and Methylibium (1.22%-3.77%), and facultative autotrophs were predominant. PCoA and LEfSe analyses revealed the differences in soil carbon sequestration microbial communities among the three forest types of tropical rainforest, with marker species belonging to Actinomycetes, γ-Proteobacteria, α-Proteobacteria and β-Proteobacteria, respectively. RDA analysis showed that total nitrogen, total phosphorus, organic carbon and readily oxidizable carbon were important soil factors for the differences.