Internal waves (IWs) are small-scale physical processes that occur frequently in stratified marginal seas. IWs are ubiquitous and well documented in the northern South China Sea (nSCS), but few studies have explored the ecosystem responses to the IWs. MODISA chlorophyll-a (Chl-a) data from 2002 to 2014 were used to examine the distribution of Chl a near the Dongsha Atoll (DSA). Composite Chl a from about 40 IWs during spring and summer showed stronger response on the northern side than on the southern side of the DSA. One day after the passage of IWs, composite surface Chl a on the northern side increased from 0.11 mg/m3 to a maximum mean value of 0.18 mg/m3 . It decreased to 0.13 mg/m3 after two days and maintained that level for several days after the passage of IWs. The enhanced surface Chl a likely caused subsurface Chl-a maximum and nutrients in the surface layer. Approximately 64% of the increase in surface Chl a was due to the uplift of the subsurface Chl-a maximum one day after the passage of IWs, while nutrient-induced new phytoplankton growth contributed about 18% of the increase a few days later. 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 the DSA than on the south, which caused a north-south asymmetric distribution of Chl a in the region.