Soil microbial communities are the key drivers of nutrient cycling in ecosystems. However, the functional response of soil microbial community composition to contrasting vegetation types in tropical coral islands is still unclear. Tropical coral islands provide a unique, extreme habitat characterized by higher soil pH and P, but lower N and soil water contents. To determine the responses of soil microbial communities to changes in vegetation types, soil microbial biomass and community composition were investigated by determination of phospholipid fatty acids (PLFAs) under three vegetation types (including tree, shrub, and herb-vine) on Dong Island and Yongxing Island of southern China. Redundancy analysis (RDA) has been used to determine the driving factors (soil properties) for shaping soil microbial community composition. The results showed that the total biomass of PLFAs, as well as the specific microbial taxa [such as bacteria, Gram-positive bacteria (G⁺), Gram-negative bacteria (G^-), fungi, arbuscular mycorrhizal fungi (AMF), and actinomycetes] increased in the soils from herb-vine via shrub to tree. Furthermore, along the above vegetation types gradient, the ratios of Gram-positive to Gram-negative bacteria (G⁺:G^-), total saturated to total monounsaturated fatty acids (sat:mono), and fungi to bacteria (F:B) ratio decreased, indicating a shift in soil microbial community towards lower stress and copiotrophic dominance. Our findings indicate that soil microbial groups have a sensitive response to shifting plant communities in tropical coral islands, and soil water content, the ratios of soil organic matter and N content to P content, and soil pH might be the critical drivers of microbial community composition and structure in the study region.