​The growth of phytoplankton and thus marine primary productivity depend on photophysiological performance of phytoplankton cells that respond to changing environmental conditions. The South China Sea SCS is the largest marginal sea of the western Pacific and plays important roles in modulating regional climate and carbon budget. However, little has been documented on photophysiological characteristics of phytoplankton in the SCS. For the first time, we investigated photophysiological characteristics of phytoplankton assemblages in the northern South China Sea NSCS using a real-time in-situ active chlorophyll a fluorometry, covering 4.0 × 105 km2. The functional absorption cross section of photosystem II PSII in darkness (σPSII) or under ambient light (σPSII’) (A2 quanta-1) increased from the surface to deeper waters at all the stations during the survey period 29Julyto23August2012. While the maximum Fv/Fm,measuredindarkness or effective Fq′/Fm′,measuredunderambientlight photochemical efficiency of PSII appeared to increase with increasing depth at most stations, it showed inverse relationship with depth in river plume areas. The functional absorption cross section of PSII changes could be attributed to light-adapted genotypic feature due to niche-partition and the alteration of photochemical efficiency of PSII could be attributed to photo-acclimation. The chlorophyll a fluorometry can be taken as an analog to estimate primary productivity, since areas of higher photochemical efficiency of PSII coincided with those of higher primary productivity reported previously in the NSCS.