Abstract: Diatoms are one of the most important groups of marine phytoplankton. Warming and nutrient limitation are the most important limiting factors affecting the growth and metabolism of marine diatoms in contemporary oceans. However, the effects of their complex interaction on diatoms have received little attention. In this study, the marine model diatom Phaeodactylum tricornutum was used as the research material, and the growth, physiological indexes, and expression of nutrient limitation marker genes were measured under different temperature and nutrient concentration conditions. The results showed that the effect of nitrogen and phosphorus nutrient limited on the growth of algal cells was increased by warming, while the effect of iron limitation was reduced. The gene expression analysis further verified the difference between the interaction of warming and limitation of macro elements (nitrogen and phosphorus), and interactive effects of microelement (iron) limitation. The above results reveal that the physiological response of diatoms to the interaction between warming and nutrient limitation is not consistent. In the context of global warming, rising temperature may strengthen the nitrogen and phosphorus limitation of diatoms, but reduce the iron limitation, thus affecting the change trend of primary productivity in different sea areas.