Marine heatwaves (MHWs) are extreme weather events that have major impacts on the structure and functioning of marine ecosystems worldwide. Due to anthropogenic climate change, the occurrence of MHWs is predicted to increase in the future. There is already evidence linking MHWs with reductions in biodiversity and incidence of mass mortality events in coastal ecosystems. However, because MHWs are unpredictable, the quantification of their effects on communities is challenging. Here, we use the Helgoland Roads long-term time series (German Bight, North Sea), one of the richest marine time series in the world, and implement a modified before-after control-impact (BACI) design to evaluate MHWs effect on mesozooplankton communities. Mesozooplankton play an essential role in connecting primary producers to higher trophic levels, and any changes in their community structure could have far-reaching impacts on the entire ecosystem. The responses of mesozooplankton community to MHWs in terms of community structure and densities occurred mainly in spring and autumn. Abundances of seven taxa, including some of the most abundant groups (e.g., copepods), were affected either positively or negatively in response to MHWs. In contrast, we observed no clear evidence of an impact of summer and winter MHWs; instead, the density of the most common taxa remained unchanged. Our results highlight the seasonally dependent impacts of MHWs on mesozooplankton communities and the challenges in evaluating those impacts. Long-term monitoring is an important contributor to the quantification of effects of MHWs on natural populations.