Zooplankton are the primary energy pathway from phytoplankton to fish. Yet, there is limited understanding about how climate change will modify zooplankton communities and the implications for marine food webs globally. Using a trait-based marine ecosystem model resolving key zooplankton groups, we find that future oceans, particularly in tropical regions, favour food webs increasingly dominated by carnivorous (chaetognaths, jellyfish and carnivorous copepods) and gelatinous filter-feeding zooplankton (larvaceans and salps) at the expense of omnivorous copepods and euphausiids. By providing a direct energetic pathway from small phytoplankton to fish, the rise of gelatinous filter-feeders largely offsets the increase in trophic steps between primary producers and fish from declining phytoplankton production and increases in carnivorous zooplankton. However, future fish communities experience reduced carrying capacity from falling primary production, and less nutritious food as environmental conditions increasingly favour gelatinous zooplankton, slightly exacerbating projected declines in small pelagic fish biomass in tropical regions by 2100. By bridging the gap between plankton and fish, the trait-based modelling framework used here is a powerful way to generate new insights into how climate change will impact zooplankton and the pivotal role they play in the world’s marine ecosystems.