Biological invasion significantly altered the composition of functional microbial communities in the soil, thereby affecting the nutrient absorption and community structure of native plants. Tropical coral islands were extremely susceptible to plant invasions due to the simple community structure and nutrient limitations, which in turn interfered with functional microorganisms. This study took the tropical coral island ecosystems as the research object, using bare land without plant colonization as a control, rhizosphere soils from 8 invasion plants and 2 native plants were collected. This study investigated the effects of invasion and native plants on coral island rhizosphere functional microbial communities (including arbuscular mycorrhizal fungi (AMF) and diazotrophs (nifH)) using high-throughput sequencing. Besides, the underlying driving factors on functional microbial diversity, community composition, and subnet topological parameters were also evaluated by redundancy analysis (RDA). The results showed that: 1) Colonization by both invasive and native plants significantly altered the α-diversity of functional microbial communities in the coral island soils. Specifically, AMF richness index was significantly higher in the rhizosphere soils of native plants than in invasive plants' rhizosphere soils and bare land (P < 0.05). The Shannon-Wiener index of AMF showed native plants>bare land (P < 0.05), but exhibited no significant difference versus invasive plants. For nifH, both richness and Shannon-Wiener indices showed invasive plants>control ≈ native plants (P < 0.05). Besides, significant α-diversity variations of both AMF and nifH were also observed among the rhizospheres of eight invasive species. 2) Invasive and native plants significantly changed AMF and nifH β diversity (P < 0.05). Compared with the native plants, invasive plants significantly modified subnet topological parameters (degree and average path length) for AMF, nifH, and AMF+nifH networks (P < 0.05), but did not alter betweenness centralization (P>0.05). 3) RDA showed that the α diversity and community structure of AMF and nifH were mainly affected by the soil available nitrogen, phosphorus, and plant leaf N and P content. In contrast, the subnet topological parameters were mainly driven by leaf carbon, soil organic carbon and ammonium nitrogen. In summary, the rapid invasion of harmful plants impacted the α-diversity of functional microbes (AMF and diazotrophs) in opposite trends, but significantly altered the community structure and subnet topological parameters of their co-occurrence networks on the tropical coral islands. This study provided a theoretical and practical reference for the rapid construction of above-ground and below-ground communities, soil restoration and the prevention and control of harmful plants on tropical coral islands.