The influences of ocean warming on marine lives have accelerated over the 21st century, greatly altering the structure and function of marine food webs and causing distributional shifts, species invasions, and changes in productivity. It is imperative to clarify the overall ecosystem responses to ocean warming and develop fisheries management strategies adaptive to the ecosystem changes. In this study, the potential impacts of ocean warming on trophic structure, energy flows, and fisheries production of an overexploited ecosystem were examined, and the effectiveness of fisheries management in mitigating warming impacts were also evaluated. We constructed a mass-balance food web model in Haizhou Bay and simulated three climate scenarios (RCPs 2.6, 4.5, and 8.5) along with different levels of fishing pressure, in order to examine the ecosystem responses to the combined changes in fishing and climate changes. Results showed that the total biomass of commercial species and fisheries catches would decline with rising temperature, especially under the RCP8.5 scenario. Ocean warming could induce lower trophic transfer efficiency and decrease energy recycling capacity within the food web, leading to large losses in total biomass and total production. Reducing fishing intensity could help mitigate the negative effects of ocean warming on fisheries productivity, but was insufficient to maintain ecological properties. Moreover, the effectiveness of such alternative measures would be diminished with increased greenhouse gas emissions, especially under the climate scenario of RCP8.5. The findings of this study highlight the need to slow the rise of sea temperature and implement climate-adaptive fisheries management in the future.