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Extreme weather events (EWEs; for example, heatwaves, cold spells, storms, floods and droughts) and non-native species invasions are two major threats to global biodiversity and are increasing in both frequency and consequences. Here we synthesize 443 studies and apply multilevel mixed-effects metaregression analyses to compare the responses of 187 non-native and 1,852 native animal species across terrestrial, freshwater and marine ecosystems to different types of EWE. Our results show that marine animals, regardless of whether they are non-native or native, are overall insensitive to EWEs, except for negative effects of heatwaves on native mollusks, corals and anemone. By contrast, terrestrial and freshwater non-native animals are only adversely affected by heatwaves and storms, respectively, whereas native animals negatively respond to heatwaves, cold spells and droughts in terrestrial ecosystems and are vulnerable to most EWEs except cold spells in freshwater ecosystems. On average, non-native animals displayed low abundance in terrestrial ecosystems, and decreased body condition and life history traits in freshwater ecosystems, whereas native animals displayed declines in body condition, life history traits, abundance, distribution and recovery in terrestrial ecosystems, and community structure in freshwater ecosystems. By identifying areas with high overlap between EWEs and EWE-tolerant non-native species, we also provide locations where native biodiversity might be adversely affected by their joint effects and where EWEs might facilitate the establishment and/or spread of non-native species under continuing global change.