A La Niña event is one of the strong signals of global climate anomalies. Understanding the consequences of La Niña event to marine ecosystems is important for improving fisheries stock assessment in the East China Sea. We compared species composition and the species diversity in winter between a normal year (2004) and a La Niña year (2008) in an offshore area of the East China Sea in winter using data collected from fisheries-independent bottom trawl survey. The number of observed species increased from 45 to 61 after the occurrence of La Niña. The number of warm water species decreased whereas warm temperature species increased. Though the dominant species composition only varied slightly, the stock density per station changed significantly. The stock density per station of warm water species such as Trichiurus japonicus decreased significantly whereas the stock density of warm temperature species such as Larimichthys polyactis tended to increase. Between the December of 2004 and 2008, the species richness indexes (R) increased from 1.56 to 1.92, the Shannon-Wienner diversity indexes (H′) increased from 1.23 to 1.42, and the Peilou evenness indexes(J′) increased from 0.51 to 0.57. There were no significant differences between the diversity indices accross the whole study area between 2004 and 2008. If the study area was divided into two parts, there was significant difference in the diversity indices between a normal year and a La Niña year in the southern region but not the northern region. The fishing pressure remained relatively stable during this period so the variability in fish community structure can likely be attributed to the change in climate in the East China Sea. The pattern and mechanism of the eco-response to the occurrence of La Niña events varies with the domain. Interdisciplinary studies are needed to improve our understanding of such events in the ecosystem.