The processes that cause long-term changes and abrupt community shifts (ACSs) in ecosystems are poorly understood despite decades of research. This paper presents a model that aims to explain and predict ACSs at the global scale using 14 multi-decadal time series of marine metazoans from zooplankton to fish, spanning all latitudes and the shelf to the open ocean. The paper finds that ACS coincide with changes in climate that alter local thermal regimes, which in turn interact with the thermal niche of species to trigger long-term and sometimes abrupt shifts at the community level. A large-scale ACS is predicted after 2014—unprecedented in magnitude and extent—coinciding with a strong El Niño event and major shifts in Northern Hemisphere climate. This paper concludes by underlining the sensitivity of the Arctic Ocean, where unprecedented melting may reorganize biological communities, and increase the size and consequences of ACS events in a warming world.