Predator and prey α-diversity are often positively associated; yet, underlying mechanisms remain unclear. We attempt to address this issue by deciphering how α-diversity of predator and prey influences each other’s community assembly processes and subsequently determines α-diversity. The occurrence of assembly processes were indicated by the mean pairwise taxonomic index within a community (αMPTI), assuming assembly processes left traceable imprints on species’ phylogeny. Specifically, αMPTI quantifies deviations of observed phylogenetic distances from that of random, thus indicating that non-random/deterministic assembly processes are in action. Less negative αMPTI, which hints at the occurrence of weaker homogeneous deterministic assembly processes, is expected to increase α-diversity of the community. We hypothesize that higher predator and prey α-diversity make each other’s αMPTI less negative, which then increases their α-diversity. To test the hypothesis, we calculated Shannon diversity and αMPTI for heterotrophic nanoflagellates (HNF; predator) and bacteria (prey) communities in the East China Sea. The HNF Shannon diversity was found to make the αMPTI of bacteria less negative, which then increased bacterial Shannon diversity. In contrast, bacterial Shannon diversity did not affect HNF’s αMPTI. We provide evidence that top-down control underpins the positive α-diversity association among trophic levels in microbes of the East China Sea.