Vegetation and associated soil microbial community play important roles in the maintenance of the function and stability of tropical coral island ecosystems. In this study, we collected different soil samples from a tropical coral island at the preliminary stage of plant community establishment. These soil samples included bulk soils before and after plant establishment (coral sand), nutrition soils used during planting (nutrition soils), and the bulk and rhizosphere soils of the transplanted seedlings in the nursery (nursery bulk and rhizosphere soils). Using amplicon sequencing, we assessed and compared the diversity, composition, and variation of fungal and bacterial communities among the four types of soil samples. Our results showed that the nutrition soils, nursery bulk and rhizosphere soils were important sources for microbial community restoration in coral sands. The major fungal phylums in these soils included Ascomycota and Zygomycota, while the major bacterial phylums included Proteobacteria and Acidobacteria. Fungal richness was significantly lower in coral sands (864.2±41.4) than in nursery rhizosphere (1086.1±64.3, P=0.014) and nursery bulk soils (1251.4±48.1, P < 0.001). However, no significant difference in the bacterial richness was detected among these soils. The establishment of plant community also significantly altered the composition of both fungal and bacterial communities in the coral sands; the relative abundance of Zygomycota increased from 0.2% to 17.4%, Agaricomycetes decreased from 20.8% to 0.9%, and β-Proteobacteria decreased from 17.7% to 0.1%. Our results demonstrate that the process of microbial community restoration in the coral sands is not simply fulfilled by adding up microbial groups from the different soil sources; several microbial groups with lifestyles being closely associated with plants were not predominant in the coral sands. Furthermore, some microbial groups with lower relative abundances in the seedling soil samples were dominant in coral sands, suggesting that the soil microbial community restoration was complex.