Ocean warming is driving significant changes in the structure and functioning of marine ecosystems, shifting species' biogeography and phenology, changing body size and biomass and altering the trophodynamics of the system. Particularly, extreme temperature events such as marine heatwaves (MHWs) have been increasing in intensity, duration and frequency. MHWs are causing large-scale impacts on marine ecosystems, such as coral bleaching, mass mortality of seagrass meadows and declines in fish stocks and other marine organisms in recent decades. In this study, we developed and applied a dynamic version of the EcoTroph trophodynamic modelling approach to study the cascading effects of individual MHW on marine ecosystem functioning. We simulated theoretical user-controlled ecosystems and explored the consequences of various assumptions of marine species mortality along the food web, associated with different MHW intensities. We show that an MHW can lead to a significant biomass reduction of all consumers, with the severity of the declines being dependent on species trophic levels (TLs) and biomes, in addition to the characteristics of MHWs. Biomass of higher TLs declines more than lower TLs under an MHW, leading to changes in ecosystem structure. While tropical ecosystems are projected to be sensitive to low-intensity MHWs, polar and temperate ecosystems are expected to be impacted by more intense MHWs. The estimated time to recover from MHW impacts is twice as long for polar ecosystems and one-third longer for temperate biomes compared with tropical biomes.This study highlights the importance of considering extreme weather events in assessing the effects of climate change on the structures and functions of marine ecosystems.