Global warming and imbalances in nitrogen (N)-phosphorus (P) ratios due to increased human activity have had significant impacts on coral reef ecosystems. However, the underlying mechanisms of these impacts remain poorly understood. In this study, a controlled experiment was conducted on Acropora hyacinthus treated with different P concentrations at high temperature (30 °C) and high N level (9 μM nitrate), which was analyzed in terms of physical observations and physiological indices, as well as photosynthetic activity and fatty acid composition. The results indicated that nitrate enrichment significantly reduced Symbiodiniaceae density, total chlorophyll content, and photosynthetic efficiency, as well as notable coral bleaching. P addition alleviated some of these detrimental effects, enhancing symbiotic relationship and maintaining photosynthetic activity. Additionally, changes in fatty acid composition suggest that P supplementation may improve coral tolerance to the combined stress of heat stress and nitrate enrichment by enhancing coral heterotrophy. These findings underscore the importance of balanced nutrient ratio for corals and propose P supplementation as a potential strategy to mitigate the combined stress on coral reefs.