Mesoscale eddies have been suggested to have an impact on biological carbon fixation in the South China Sea(SCS). However, their overall contribution to primary production during the spring inter-monsoon period is still unknown. Based on large-scale biological and environmental in situ observations and synchronous remote sensing data, the distribution patterns of phytoplankton biomass and the primary production, and the role of mesoscale eddies in regulating primary production in different eddy-controlled waters were investigated. The results suggested that the surface chlorophyll a concentrations and water column integrated primary production(IPP) are significantly higher in cyclonic eddies and lower in the anticyclonic eddies as compared to that in non-eddy waters. Although eddies could affect various environmental factors, such as nutrients, temperature and light availability, nutrient supply is suggested to be the most important one through which mesoscale eddies regulated the distribution patterns of phytoplankton biomass and primary production. The estimated IPP in cyclonic and anticyclonic eddies are about 29.5% higher and 16.6% lower than the total average in the whole study area, respectively, indicating that the promotion effect of mesoscale cold eddies on the primary production was much stronger than the inhibition effect of the warm eddies per unit area. Overall, mesoscale eddies are crucial physical processes that affect the biological carbon fixation and the distribution pattern of primary production in the SCS open sea, especially during the spring inter-monsoon period. Mesoscale eddies have been suggested to have an impact on biological carbon fixation in the South China Sea (SCS). However, their overall contribution to primary production during the spring inter-monsoon period is still unknown. Based on large-scale biological and environmental in situ observations and synchronous remote sensing data, the distribution patterns of phytoplankton biomass and the primary production, and the role of mesoscale eddies in regulating primary production in different eddy-controlled waters were investigated. The results suggested that the surface chlorophyll a concentrations and water column integrated primary production (IPP) are significantly higher in cyclonic eddies and lower in the anticyclonic eddies as compared to that in non-eddy waters. Although eddies could not affect various environmental factors, such as nutrients, temperature and light availability, nutrient supply is suggested to be the most important one through which mesoscale eddies regulated the dist ribution patterns of phytoplankton biomass and primary production. The estimated IPP in cyclonic and anticyclonic eddies are about 29.5% higher and 16.6% lower than the total average in the whole study area, respectively, indicating that the promotion effect of mesoscale cold eddies on the primary production was much stronger than the inhibition effect of the warm eddies per unit area. Overall, mesoscale eddies are crucial physical processes that affect the biological carbon fixation and the distribution pattern of primary production in the SCS open sea, especially during the spring inter-monsoon period.