Climate change is affecting ocean temperature, acidity, currents, and primary production, causing shifts in species distributions, marine ecosystems, and ultimately fisheries. Earth system models simulate climate change impacts on physical and biogeochemical properties of future oceans under varying emissions scenarios. Coupling these simulations with an ensemble of global marine ecosystem models has indicated broad decreases of fish biomass with warming. However, regional details of these impacts remain much more uncertain. Here, we employ CMIP5 and CMIP6 climate change impact projections using two Earth system models coupled with four regional and nine global marine ecosystem models in 10 ocean regions to evaluate model agreement at regional scales. We find that models developed at different scales can lead to stark differences in biomass projections. On average, global models projected greater biomass declines by the end of the 21st century than regional models. For both global and regional models, greater biomass declines were projected using CMIP6 than CMIP5 simulations. Global models projected biomass declines in 86% of CMIP5 simulations for ocean regions compared to 50% for regional models in the same ocean regions. In CMIP6 simulations, all global model simulations projected biomass declines in ocean regions by 2100, while regional models projected biomass declines in 67% of the ocean region simulations. Our analysis suggests that improved understanding of the causes of differences between global and regional marine ecosystem model climate change projections is needed, alongside observational evaluation of modeled responses.