Biological productivity in the summer Vietnam boundary upwelling system in the western South China Sea, as in many coastal upwelling systems, is strongly modulated by wind. However, the role of ocean circulation and mesoscale eddies has not been elucidated. Here we show a close spatio-temporal covariability between primary production and kinetic energy. High productivity is associated with high kinetic energy, which accounts for ~ 15 % of the production variability. Results from a physical-biological coupled model reveal that the elevated kinetic energy and intensified circulation can be explained by the separation of the upwelling current system. The separated current forms an eastward jet into the interior South China Sea, and the associated southern gyre traps nutrient and favors productivity. When separation is absent, the model shows weakened circulation and eddy activity, with ~ 21 % less nitrate inventory and ~ 16 % weaker primary productivity.