Understanding predator-prey biodiversity relationship has been an important issue for ecology. Here, for the first time, we examined the biodiversity relationship and its consequences on trophic interaction between nanoflagellates (predators) and bacteria (prey) in the East China Sea. We obtained the nanoflagellates and bacterial biodiversity data through the sequences of 18S and 16S rDNA respectively with illumina Miseq, and abundance data by using epifluorescence microscopic and flow cytometry counting, respectively. Specifically, we evaluate the relationship between nanoflagellates and bacteria biodiversities and abundances after accounting for the environmental variables with linear regression. Our results indicate that predator and prey diversity were positive related, and prey abundance increased with decreasing predator/prey biodiversity ratio, indicating that consumption of predators decreased with increasing prey diversity and decreasing predator diversity. Our results indicate that the bottom-up and top-down processes interactively controls bacterioplankton and nanoflagellates communities in the East China Sea.