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• We built and calibrated a multispecies size-spectrum model for mixed fisheries ecosystem. • Observed biomass was used to evaluate model performance. • Larimichthys crocea was the greatest beneficiary under increasing gear selectivity or reducing fishing effort. • Trade-offs exist between long-term ecological benefits and short-term economic losses. • Ecosystem-Based Fisheries Management (EBFM) is more effective with combined strategies. Multispecies mixed fisheries involve complex species interactions and ecosystem dynamics, posing remarkable challenges for identifying effective fishery management strategies. Although gear selectivity and fishing effort have become common and crucial measures in managing mixed fisheries, their ecological effects and trade-offs remain poorly understood from the perspective of species interactions and ecosystems. Based on bottom trawl survey data collected between 2020 and 2021 in the offshore waters of southern Zhejiang (OWSZJ), we built and calibrated a multispecies size-spectrum model (MSSM) for this mixed fishery ecosystem. Species observed biomass from the survey was used to evaluate model performance. We explored the effects of increasing gear selectivity and reducing fishing effort at population and community levels. We found that Larimichthys crocea and Lophius litulon were the main beneficiaries under these strategies. In particular, L. crocea showed the most pronounced increases in biomass and yield. Model projections indicated that changes in fishing effort not only had a greater effect on total biomass and community size structure than changes in gear selectivity but also led to yield losses for many commercial species. Our results suggest that no single strategy is universally optimal across all species, and each management strategy involves trade-offs between fishery yields and rebuilding depleted stocks. A combined approach integrating both strategies may offer the greatest potential for achieving ecological benefits and socio-economic outcomes. This study provides scientific support and insights for the application of Ecosystem-Based Fisheries Management (EBFM) in mixed fisheries.