Silicon (Si), as one of the important components of the global biogeochemical cycles, is of great significance to the primary productivity dominated by phytoplankton and the silicon and carbon cycles in marine ecosystem. It is well known that diatoms dominate the silicon cycle of the global ocean, and become an important bridge for the interaction between the silicon cycle and carbon cycle. Individual cells of Synechococcus play a key role in starting and supporting marine food web and energy flow, thus they become the main contributors in global carbon cycle, recently, they were also found to have important function in Si accumulation, which provides us a new perspective in silicon and carbon cycles in open ocean in addition to diatoms, however, the discovery of Si accumulation by marine Synechococcus shows a large challenge to the absolute position of diatoms in the global silicon and carbon cycles. For such a huge biomass of Synechococcus in the ocean, even higher than that of diatoms, it is necessary to understand what is the mechanism of carbon sinking and to accurately simulate its silicon cycle, nevertheless, the researches on Si accumulation by marine Synechococcus are very rare, the mechanism of Si absorption and storage as well as the role of regulation mechanism are not clear. In addition, its regulatory effect on the silicon carbon cycle has not been reported. Therefore, based on the previous studies in Si accumulation of individual cells of Synechococcus, we hope that there will be a basic understanding of Si accumulation by marine Synechococcus and their regulatory mechanism of silicon and carbon cycles in marine ecosystem.