To investigate the effect of seasonal marine environment conditions on the cyanobacteria abundance and diversity in the South Sea, four-seasonal surveys were conducted along the 127.5°E survey transect line in the central South Sea using flow cytometry and 16S-23S ITS on the Miseq platform from August 2016 to May 2017. The average abundance of Synechococcus varied from 3.3 × 103 to 7.4 × 104 cells ml-1. The abundance was the highest in the summer and the lowest in the winter, and the abundance fluctuated according to water temperature. The abundance was high in the outer sea affected by TWC. However, in summer, the Coastal areas affected by the Yangtze River were more populated than the outer sea. Prochlorococcus was rare and could not penetrate into coastal areas due to the fronts, but showed its dominance in the waters influenced by the TWC. Synechococcus clades II, VII, IX, CRD1, and CRD2 were predominant in the outer sea area affected by the TWC. In the coastal area, clades I and IV showed higher dominance whereas clades V, VI, WPC1, and 5.3-MS3 with euryhaline characteristics, showed a high dominance rate in the water masses affected by the low-salinity water of the Yangtze River in the summer. Clade XVI, XVII, CB1, CB5, and 5.3-I/II showed high dominance in nutrient-rich waters in the summer with increased water temperature. The abundance and community composition of cyanobacteria changed in the South Sea due to the influence of the TWC and stratification. In the summer, the abundance and the community composition differed, and were mainly affected by the general influence of the TWC in addition to the influence of the Yangtze River low-salinity water.