[Background] The interaction between marine phytoplankton-derived organic matter and heterotrophic bacteria is an important part of biogeochemistry cycle in the upper ocean. [Objective] Studying the responses of microbial communities in oligotrophic environment to Synechococcus-derived organic matter (SOM) could increase our understanding of marine biogeochemistry cycle. [Methods] A SOM-addition incubation experiment was conducted in the South China Sea, and the variations of organic carbon, nutrients, and active microbial communities were monitored during the incubation. [Results] During the short-term incubations, 60%–73% of SOM was utilized by microbes. Gammaproteobacteria was the fastest responder, and the most dominant microbial population over the entire incubations. The addition of SOM changed the in situ microbial community structure, and the succession of microbial community structure was also observed corresponding the consumption of labile organic matter. [Conclusion] Most of the SOM belong to labile organic matter which could be quickly degraded and utilized by heterotrophic bacteria. Microbes could respond positively to phytoplankton-derived fresh organic matter, and their activities drive the biogeochemistry cycle in the ocean.