Marine heatwaves (MHWs) are becoming more frequent and intense in the Southern Ocean, potentially exerting profound impacts on Antarctic marine ecosystems. However, the physiological responses of Antarctic diatoms to MHWs remain poorly understood. In this study, the Antarctic diatom Fragilariopsis cylindrus was cultured under control (0°C), moderate marine heatwave (3°C), and extreme marine heatwave (5°C) conditions in semi-continuous cultures to investigate the effects of heatwave intensity, duration (6, 12, and 18 days), and frequency (single vs. repeated events) on growth rate, cellular chlorophyll a (Chl a), and biogenic silica (BSi) content. Elevated temperature generally promoted growth, with the highest growth rates consistently observed at 5°C. During MHWs exposure, both cellular Chl a and BSi contents initially increased, peaking on day 12 under 5°C, before declining by day 18, while growth rates remained relatively high throughout the experiment. These results suggest that moderate-duration MHWs enhance the accumulation of cellular pigments and biogenic silica, whereas prolonged exposure promotes physiological acclimation, leading to a reallocation of resources toward cell growth. During the post-heatwave cooling phase, cellular Chl a and BSi increased markedly, while growth rates declined, indicating a shift toward enhanced investment in photosynthetic capacity and cellular structural reconstruction. Under repeated heatwave exposure, growth rates further increased, whereas cellular Chl a and BSi decreased compared to the first heatwave event. This pattern indicates the development of thermal acclimation, enabling cells to maintain rapid growth while reducing resource allocation to pigment synthesis and silicification. Overall, our findings demonstrate that MHWs reshape resource allocation strategies in F. cylindrus, driving a dynamic balance among growth, pigment accumulation, and silicification. Repeated MHWs events may promote population growth but reduce cellular silica content, with potential implications for the ecological function of Antarctic diatoms and the Southern Ocean silicon cycle. Future integration of transcriptomic analyses, along with measurements of particulate organic carbon (POC) and particulate organic phosphorus (POP), will help further elucidate thermal acclimation mechanisms and resource allocation strategies under future marine MHW scenarios.