Abstract: The stable carbon isotope of size fractionated zooplankton was studied in the northern South China Sea during summer and winter, 2015. The zooplankton was divided into three groups according to size structure, i.e., micro- (180–380 μm), meso- (380–500 μm) and macro- (>500 μm). Significant spatial difference of zooplankton stable carbon isotope was found. The δ¹³C value of zooplankton ranged from –24.19 to –19.57 in summer. High δ¹³C value of micro- and mesozooplankton mainly distributed in south of the survey area. The δ¹³C value of zooplankton ranged from –23.89 to –19.69 in winter, while the spatial distribution situation was opposite. No obvious seasonal and size fractionated change of δ¹³C value has been found. The δ¹³C values of size fractionated zooplankton were positively related to the numerical value of mean chlorophyll a concentration, but showed no significant correlation to zooplankton biomass.