Viral abundance in deep sea planktonic environments is surprisingly high. However, the biological, ecological and biogeochemical role of virioplankton in the deep sea is under debate. In the present study, microcosm incubations of deep sea bacterioplankton with and without virus impact were conducted in the western Pacific Ocean. We observed a significant negative effect of viruses on prokaryotic abundance, which indicated top-down control of deep sea bacterioplankton by virioplankton. Decreased bacterial diversity and a different bacterial community structure in treatments without viruses indicate that viruses are important factors for influencing bacterial diversity and sustaining a highly diverse microbial community in the deep sea. In addition, network analysis showed a strong shift of the interactions among the active microbial communities. Our study demonstrated, for the first time experimentally the impacts of virioplankton on deep sea bacterioplankton communities, suggesting the potential role of viruses for microbial ecology and biogeochemistry in deep sea ecosystem.