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Cell size of phytoplankton is known to influence their physiologies and, consequently, marine primary production. To characterize the cell size-dependent photophysiology of phytoplankton, we comparably explored the photosynthetic characteristics of piconano- (<20 µm) and micro-phytoplankton cell assemblies (>20 µm) in the Daya Bay, northern South China Sea, using a 36-h in situ high-temporal-resolution experiment. During the experimental periods, the phytoplankton biomass (Chl <i>a</i>) in the surface water ranged from 0.92 to 5.13 μg L⁻¹, which was lower than that in bottom layer (i.e., 1.83–6.84 μg L⁻¹). Piconano-Chl <i>a</i> accounted for 72% (mean value) of the total Chl <i>a</i>, with no significant difference between the surface and bottom layers. The maximum photochemical quantum yield (F_V/F_M) of Photosystem II (PS II) and functional absorption cross-section of PS II photochemistry (σ_{PS II}) of both piconano- and micro-cells assemblies varied inversely with solar radiation, but this occurred to a lesser extent in the former than in the latter ones. The σ_{PS II} of piconano- and micro-cell assemblies showed a similar change pattern to the F_V/F_M in daytime, but not in nighttime. Moreover, the fluorescence light curve (FLC)-derived light utilization efficiency (α) displayed the same daily change pattern as the F_V/F_M, and the saturation irradiance (E_K) and maximal rETR (rETR_max) mirrored the change in the solar radiation. The F_V/F_M and σ_{PS II} of the piconano-cells were higher than their micro-counterparts under high solar light; while the E_K and rETR_max were lower, no matter in what light regimes. In addition, our results indicate that the F_V/F_M of the micro-cell assembly varied quicker in regard to Chl <i>a</i> change than that of the piconano-cell assembly, indicating the larger phytoplankton cells are more suitable to grow than the smaller ones in the Daya Bay through timely modulating the PS II activity.