Internal waves (IWs) are small-scale physical processes occurring frequently in stratified marginal seas. IWs are ubiquitous in the northern South China Sea (nSCS) and well documented, but ecosystem responses to the IWs in the nSCS are less studied. MODIS chlorophyll (Chl-a) data from 2002 to 2014 are used to examine the distribution of Chl-a near Dongsha Atoll (DSA). Composite Chl-a from about 40 IWs during spring and summer shows stronger response on the northern side than on the southern side of DSA. Composite surface Chl-a on the northern side increased from 0.11 mg m-3 to the maximum mean value of 0.18 mg m-3 one day after the passage of IWs, and then decreased to 0.13 mg m-3 after two days; it maintained the level of 0.13 mg m-3 for several days after the passage of IWs. The enhanced surface Chl-a likely caused subsurface Chl-a maximum and nutrients into the surface layer. About 64% of the contribution to surface Chl-a increase was due to the uplifting of subsurface Chl-a maximum one day after the passage of IWs, while nutrients-induced new phytoplankton growth may contribute about 18% a few days afterwards. When the IWs occurred frequently in spring and summer, Chl-a level on the northern side was about 30% higher than that on the southern side. IW dissipation and its impact on nutrients and chlorophyll were stronger on the northern side of DSA, which caused the north-south asymmetric distribution of Chl-a in the region.