Merged ocean color data from 1999 to 2017 is used to analyze the chlorophyll concentration variations around the reefs and islands in the South China sea. The results show that the islands center has the highest chlorophyll concentration, which decreases with the distance increases between the islands center to outside. The concentration decreases to the value of open sea area while the distances reach to five radiuses of islands. the level of chlorophyll concentration of the islands area depends on the level of the chlorophyll concentration of the open sea area.

Moreover, the chlorophyll concentration is heavily influenced by monsoons. In winter, monsoon is cool and rapid that leads to the strong effect of ocean surface fluctuation. At that time, the chlorophyll concentration increasing significantly because of the suitable temperature of seawater, which reach to the maximum at January. When monsoon weakened, the chlorophyll concentration decreasing with the temperature of seawater increasing, which reach to the minimum at May. In summer, monsoon comes to frequent so that the chlorophyll concentration increasing again.

Annually, the chlorophyll concentration has significant correlation with Nino 3.4 index. When La Niña happened, the chlorophyll concentration at a low level and increasing gradually. When Nino 3.4 larger than 0.5, El Nino happened, the chlorophyll concentration at a high level and decreasing gradually. The high level of chlorophyll concentration depends on the duration of the trend of Nino 3.4 close to zero.