Recently, the influence of climate change on marine organisms and ecosystems has attracted attention on a global scale. In an effort to elucidate the impact of climate change on nekton community structure and on some commercial species in the northern East China Sea (NECS) during winter, we summarized the fluctuation of sea surface temperature (SST) in the offshore area of NECS from 1960-2011, and compared this to the catch data of 17 species targeted in bottom trawl fishery and to independent fishery data from the open waters of the NECS. We used Fox models to remove the effect of fishing pressure on changing population trends. Regime shift detection methods were used to identify change points in trends of production and environmental variables. Our results showed that the winter SST from 1960 to 2011 exhibited a long-term warming trend superimposed on interdecadal variability. The NECS experienced a cold period from 1960-1982, followed by a warming period from 1983 to 1998, and then a relatively stable warm period from 1999 to 2011. Changes in the community structure showed that the abundance of demersal and large predatory species was significantly negatively related to SST and the abundance of midwater species and invertebrates was positively related to SST. Abundance of large predatory species was lower in the warm period than in the cold period, while the abundance of midwater species and invertebrates was low in most of the years during 1971-1982, but increased during 1999-2011; catch of warm water species was higher in the warm period than in the cold period, but abundances were generally lower. At the same time, the Shannon diversity index was higher in the warm period than in the cold period. Upon removing the effect of fishing pressure, we found that catch per unit effort (CPUE) residuals for demersal species, midwater species and invertebrates had was positively correlated with SST, particularly the correlation between the CPUE residuals for midwater species and SST anomalies, which was significant. While CPUE residuals for large predatory species were negatively correlated with SST, CPUE residuals of warm water species/warm temperature species presented a positive/negative correlation with SST anomalies, respectively. Correlations between CPUE residuals and SST anomalies differed for commercial species based on habitat. Setipinna taty and Pampus argenteus were significantly and positively correlated with SST anomalies, while the correlation between Trichiurus japonicus, squid, and SST anomalies was positive. Larimichthys polyactis and shrimp were also positively correlated with SST anomalies. Considering the steadily warming climate, research priorities aimed at realizing the sustainable development of fishery resources should include analyzing the impact of warming temperatures on marine community structure and function, identifying variability in fishery resources in East China Sea and the mechanisms behind their responses, and developing scientific fishery management strategies.