Soft corals (order Alcyonacea), characterized by minimal or absent skeletal structures, have received far less attention compared to reef building hard corals (order Scleractinia), despite their vulnerability to heat stress. This study investigated the thermal response mechanisms of two symbiotic corals, Galaxea fascicularis (stony coral) and Clavularia inflata (soft coral), which could be found in the same water region and depth in the South China Sea. Using controlled heat stress experiments, we analyzed their photophysiological and metabolomic response. While G.fascicularis maintained stable net photosynthetic rates (Pnet) and increased dark respiration (Rd), C. inflata showed a decline in Rd, a slight Pnet reduction, and a symbiont loss. Metabolic changes in G. fascicularis were primarily focused on energy production (e.g., Dmannose, D-sorbitol, and succinate) and amino acid metabolism (e.g., D-proline, glutamic acid, and histidine). In contrast, C. inflata exhibited a broader range of metabolic shifts, including Glucosamine-6-phosphate (energy pathways), D-proline, histidine, tryptophan, and taurine (amino acid metabolism), purines and pyrimidines (nucleotide metabolism), carnosic acid, linolenic acid, and retinene (antioxidants), as well as the dipeptides His-Ser and Lys-Lys. These findings revealed that metabolic adjustments played a key role in thermotolerance in G. fascicularis, while C. inflata exhibited a more diverse response and incurred energetic costs in response to thermal stress. This research provides insights into coral resilience mechanisms, shedding light on why C. inflata may be less competitive under heatwaves and contributing to our understanding of shifts in coral reef community composition driven by climate change