Abstract: Trophic structure and trophic transfer efficiency are among the most fundamental characteristics of an ecosystem. They characterize the transfer of nutrient and energy and are crucial in estimating the yield of harvestable biomass. In this study, we investigated the regulation of trophic structure (phytoplankton, zooplankton, and larval fish abundance) and biomass ratio of zooplankton to phytoplankton (as an indicator of transfer efficiency) in the East China Sea, one of the largest marginal seas in the world and an important fishing ground. The results showed that when sea surface temperature was below 25°C, temperature co-acted with resource availability (zooplankton for larval fish and phytoplankton for zooplankton) in determining the trophic structure. When sea surface temperature was above 25°C, resource availability dominated the regulation of trophic structure. Biomass ratio of zooplankton to phytoplankton decreased with increasing phosphate concentration. Our study suggested that the trophic structure of the East China Sea might be controlled by bottom-up processes, and this control is mediated by temperature.