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Located at the margin of the Northwest Pacific Ocean, the Yellow Sea (YS) and East China Sea (ECS) marine ecosystems are mainly influenced by the Kuroshio and its branches. In addition to decadal changes in their marine environments, the YS and ECS have been impacted by intensive fishing at both the species- and community-levels, leading to over-exploitation of commercial species and changes in species composition and trophic structure. The dual effects of overfishing and climate change on the variability and processes of the YS and ECS ecosystem structure and functions are not well understood. In this study, we have compiled biological and physical time series, including 147 taxa catches, 7 local-scale environmental variables and 8 large-scale climate indices, to explore variations in ecosystem structure, and to elucidate the effects of climate change on the two regions during the period 1950-2014. Aside from fishing impacts, results show that decadal variations occurred in both the YS and ECS, with step-like changes around the mid-1960s, mid-1970s, late 1980s and late 1990s. These changes correspond well with contemporaneous climatic regime shifts in the Pacific. Climate-induced changing patterns are also evident in different fish communities, with diverse sensitivities in response to these patterns. Increasing water temperature exhibits greater effects on cold-water group than on temperate- and warm-water groups. Functional and thermal groups both show pronounced linkages with fishing effort and physical drivers, particularly with local-scale environmental variables, which highlights the importance of fishing and the validity of biological grouping in future investigation of environmental impacts on marine organisms. Our results provide evidences for climate-induced variations in over-exploited marine ecosystems and coupled "Atmosphere-Ocean-Ecosystem" influencing processes, which have important implications for ecosystem-based fisheries management in the YS and ECS.