Dipole eddies are mesoscale oceanographic features consisted of a cyclonic eddy and an anticyclonic eddy that function as a two-way biological pump, accumulating plankton production by pumping nutrient into the euphotic zone and accelerating the transport of organic matter into deep ocean, respectively. Dipoles happened frequently in the ocean with a duration from a few days to several months, resulting in significant impacts on local and global oceanic biological, ecological and geochemical processes. To better understand how dipole shape microbial community, we examined depth-resolved distributions of microbial communities across a dipole in the South China Sea. Our data demonstrated the dipole had a substantial influence on the microbial distributions and community structures both vertically and horizontally. Large Alpha- and Beta- diversity differences were observed between anticyclonic eddy and cyclonic eddy in surface and subsurface layers, consistent with distribution changes of major OTUs in the dipole with effects of uplifted, downward transported, enriched, depleted, horizontally transported. The edge of dipole might also cause strong vertical water movement indicated by Prochlorococcus and Synechococcus. Our findings suggest that dipole with its unique physical features might act as a driver for the distribution and diversity of microbial community.