Zooplankton is an important constituent in assessing ecosystem responses to global warming. The northern East China Sea is an important ecosystem for carbon cycling with a net sink of carbon dioxide. Despite their importance as a major component in carbon cycling, relatively little is known about zooplankton biomass structure and its regulating factors in the northern East China Sea. This study examined zooplankton biomass distribution pattern in the region from multiple cruises encompassing various seasons between 2004 and 2009. Results showed that zooplankton biomass exhibits less cross-shelf gradient in general with declining biomass to the eastern shelf towards the Tsushima Current Water. Size-fractionated biomass showed that the 1.0~2.0 mm size group, mostly copepods, dominated zooplankton biomass, comprising 38 to 48% of total biomass. Smaller zooplankton (0.2~1.0 mm) biomass, consisting mainly of Paracalanus spp, a particle eating herbivorous copepod, was positively related to chlorophyll-a concentration, but no relationship was established for larger zooplankton (1.0~5.0 mm). Spatially-averaged mean total zooplankton biomass was also highly related to chlorophyll-a concentration. These result suggest that the long-term trend of zooplankton biomass increase in this region is partly accounted for by the increases of phytoplankton biomass and productivity underway in the region. However, the underlying mechanisms of how sea surface warming in the study area leads to increased phytoplankton biomass and productivity remains unclear.