Stable isotope analysis has emerged as one of the primary means to analyze the structure of food webs. Size fractionated zooplankton biomass and stable isotopes in the southern South China Sea during spring and summer 2013 were investigated. The results showed that zooplankton biomass in spring was higher than those in summer at most sites (p<0.05), while the maximal value was found in the southwestern continental shelf (influenced by coastal upwelling) with increased mean value of zooplankton biomass during summer. Zooplankton was divided into three groups according to size. Macro- zooplankton contributed more to the total zooplankton biomass during summer, while meso- and micro-zooplankton contributed more during spring. Mean δ¹⁵N value in spring was higher than that in summer, and the δ¹⁵N value of macro-zooplankton was higher than those of meso- and micro-zooplankton at most sites. Zooplankton biomass was negatively related to mixed layer depth and seawater temperature at 75-m depth, and positively related to salinity at 75 m, indicating that zooplankton biomass was influenced by vertical mixing. The result of GAM (generalized additive model) indicated that the δ¹⁵N value of micro-zooplankton was affected by combined impacts by environmental and biological factors.