A distinctive seasonal pattern in phytoplankton biomass was observed at the South East Asian Time‐series Study (SEATS) station (18°N, 116°E) in the northern South China Sea (SCS). Surface chlorophyll‐a, depth‐integrated chlorophyll‐a and primary production were elevated to 0.3 mg/m3, ∼35 mg/m2 and 300 mg‐C/m2/d, respectively, in the winter but stayed low, at ≤0.1 mg/m3, ∼15 mg/m2 and 110 mg‐C/m2/d as commonly found in other low latitude waters, in the rest of the year. Concomitantly, soluble reactive phosphate and nitrate+nitrite in the mixed layer also became readily detectable in the winter. The elevation of phytoplankton biomass coincided approximately with the lowest sea surface temperature and the highest wind speed in the year. Only the combined effect of convective overturn by surface cooling and wind‐induced mixing could have enhanced vertical mixing sufficiently to make the nutrients in the upper nutricline available for photosynthetic activities and accounted for the higher biomass in the winter.