Community composition is determined largely by drift, selection, dispersal, and speciation. The crucial issue is disentangling the relative importance of different processes in community assembly. However, this issue has not been adequately discussed in benthic foraminiferal communities. Here, we studied the community composition, co-occurrence network, and community assembly of benthic foraminifera (protozoa) on the Xisha carbonate platform and their coupled relationships. The community composition was determined via the environmental DNA (eDNA) technique. Heavy metals, grain sizes, loss on ignition (LOI), organic carbon, and pH were measured for environmental assessment. The results showed that spatial variations in foraminiferal community composition were mainly controlled by organic carbon, whereas the effects of other variables were minimal. Similarly, spatial variations in the co-occurrence network were determined by organic carbon and pH. Despite the impacts of environmental variables on community composition, null and neutral models demonstrated that foraminiferal community assembly is driven by ecological drift instead of selection. This study is the first to couple community composition and co-occurrence networks with community assembly processes. A hypothesis was proposed that selection increases community heterogeneity and network heterogeneity, whereas stochastic processes eliminate such heterogeneities. This mechanism would bridge the gap between processes and community patterns. A comparison with our previous study revealed that foraminiferal community assembly may depend on specific systems (habitats). This insight could inform new strategies for the conservation of marine biodiversity.