ABSTRACT Diatoms play important roles in ocean primary production, the biological carbon pump and global carbon cycles. Their biomass is often limited by iron (Fe) in most ocean waters and is widely affected by global warming. However, the interactive effect of warming and Fe limitation on diatoms has not yet been revealed. Here, we found that Fe limitation inhibited the growth of Phaeodactylum tricornutum , but this inhibition could be alleviated by warming. Fe limitation combined with warming affected most metabolic pathways, including ribosomes, Fe acquisition, photosynthesis and respiration. However, the strategies of P. tricornutum response to warming varied across different temperature ranges under Fe limitation. Under Fe limitation, P. tricornutum enhances catabolism via upregulating the proteolytic pathway while suppressing ribosome biosynthesis/assembly when the temperature is elevated from sub‐ T opt to T opt , but conversely upregulates the ribosome biosynthesis/assembly and suppresses the catabolism pathways when the temperature is elevated from T opt to super‐ T opt . These findings revealed that the varied mechanisms of marine diatoms' response to the interaction of Fe limitation and warming depended on the difference between the habitat temperature and their optimal temperatures. Our results provide new insights into the changing trends in diatoms' responses to global warming in Fe‐limited regions, with significant implications for ocean productivity and marine biogeochemical cycles in a future changing climate.