Marine phytoplankton are subjected to a wide range of environmental heterogeneity from mean climate change to <br /> natural fluctuations under the climate change scenario. These changes include the changes in the frequency of temperature fluctuations of the sea surface. Here we conducted semi-continuous incubation experiments on two ecologically significant marine diatom species, <em>Thalassiosira</em> sp. and <em>Nitzschia closterium</em> f. minutissima, to examine the physiological responses to ocean warming and temperature fluctuation (±4 °C) under low (20 °C) and high (25 °C) average temperatures. Our results demonstrate that temperature fluctuation alleviated the negative effects of elevated temperatures on the growth of both species. For <em>Thalassiosira</em> sp., warming under constant temperature significantly reduced the growth rate, but significantly increased the cellular elemental contents, and sinking rate. However, warming significantly decreased the cellular particulate organic carbon (POC) and biogenic silica (BSi) contents, and sinking rate, while increasing protein content to cope with the thermal stress under temperature fluctuation. Temperature fluctuation at low average temperatures significantly increased the cellular POC and BSi contents, as well as POC productivity and sinking rate, while at high average temperatures, these parameters were significantly decreased. For <em>Nitzschia closterium</em> f. minutissima, warming under both constant and fluctuated temperatures significantly increased the POC, particulate organic nitrogen (PON) and POP quotas. The interaction between warming and temperature fluctuation had antagonistic effects on most parameters examined for <em>Thalassiosira</em> sp.; whereas had synergistic effects on the physiological parameters of <em>Nitzschia closterium</em> f. minutissima. Overall, <em>Nitzschia closterium</em> f. minutissima exhibited stronger tolerance to warming and temperature fluctuation, suggesting species-specific responses of diatoms to warming and temperature fluctuations. Overall, these findings highlight the important, yet often underestimated, influence of temperature fluctuation on the physiology of marine diatoms in the context of global warming, thus having implications for further understanding the biogeochemical feedbacks.