The volcanic island, Kueishan Island, harbors two unique shallow-water ecosystems: hydrothermal vents and coral communities. The unique geologic features render the island an ideal place as a spectrum for studying two different ecosystems and mimicking the impacts of climate change on coral reef biota in the future. However, little is known about the meiofauna community there. Hence, we investigated the diversity and composition of free-living marine nematodes over two years by collecting individuals from sediments sampled across a gradient of habitats, including hydrothermal vents, buffering sites, and coral reefs. During the first year, we also monitored abiotic factors, such as sediment and water properties, along with biotic factors, including bacterial diversity assessed through amplicon sequencing, to evaluate their influence on the nematode community. Our findings revealed markedly low nematode abundance and diversity at sulfide-rich vent sites (abundance < 5 ind./L; Shannon index < 1) throughout the study period, contrasting with the highest levels observed at the coral community site (<165.4 ind./L, Shannon index = 1.65). The food supply seemed to be the main factor that drove the difference, as nematode abundance and diversity increased with sedimentary total organic carbon and bacterial diversity. In addition, significant differences in nematode composition were observed between the different sampling sites. Combined with nematode and microbiome data, the buffering site that endured more stress from vent activities was recognized. Our results suggest that the dynamics of nematode communities could be incorporated into projects assessing environmental impacts on coral reef ecosystems.